Childhood medulloblastoma:

From genomics to improved therapies

Steve Clifford PhD

Medulloblastoma

~ 10% of UK childhood cancer deaths

Medulloblastoma:

Challenges and Goals

To improve outlook through :

Optimization and individualisation of current therapies

Maximisation of efficacy

Minimisation of side-effects

Development of new therapeutic approaches

Research Strategy

Clinical TrialsDevelopmental

Therapeutics

Exploratory Biology:

Biomarker and

Target Discovery

Translational research focused on improving

cancer therapy

Exploratory Biology:

Biomarker and Target

Identification

Li-Fraumeni syndrome family

S Clifford

Rare cancer syndromes identify genes commonly

mutated in sporadic medulloblastoma

APC in 5% of cases

PTCH in 10% of cases

TP53 in 10% of cases

S Clifford

• Define extent of pathway involvement

• Clarify clinical, pathological and functional significance

• Identify testable markers, drug targets

5%

5%

5%

5%10%

10%

Nucleus

Developmental signalling pathways in

medulloblastoma

S Clifford

The SHH signalling pathway in

cerebellar development

Romer, J and Curran, T (2005). Cancer Research. 65: 4975.

SHH and Wnt/Wg

medulloblastoma subgroups

S Clifford

The medulloblastoma transcriptome:

Disease Sub-Classification

WNT SHH

Detailed molecular

characterisation of Wnt/Wg-active

medulloblastomas

S Clifford

Chromosomal defects in medulloblastomas

19 20 21 22 X Y

Genomic analysis (array CGH):

Wnt/Wg sub-group medulloblastomas

• Monosomy 6 in all cases

• No evidence of

characteristic

medulloblastoma aberrations

(chr 7, 9, 16, 17 etc.)

• Few other defects

• Assessed 19 medulloblastomas

• Wnt/Wg activation

(b-catenin IHC; CTNNB1, APC

mutation)

• Associated chromosomal

defects

S Clifford

Cluster analysis of

genomic defects in

medulloblastomas

• Wnt/Wg-active

medulloblastomas represent a

distinct molecular disease sub-

group

S Clifford

DNA methylation, CpG islands

and epigenetic gene inactivation in cancer

Lindsey et al, 2005 Jones & Baylin. Nat Rev Genet., 2002

Wnt/Wg pathway activation and

chromosome 6 loss define a

distinct molecular sub-group of

medulloblastomas

S Clifford

Detailed molecular

characterisation of SHH-active

medulloblastomas

S Clifford

Desmoplasia and medulloblastoma

Rutkowski et al. NEJM, 2005

3-16 yrs: 5% of cases

<3yrs: 57% of cases

McManamy et al. Brain Pathol., 2006

Global analysis of the medulloblastoma epigenome:

Subgroup specific inactivation of COL1A2

A molecular sub-classification of

medulloblastoma

Pathway activation Wnt/Wg SHH ???

Major mutational

targets CTNNB1 PTCH1 ???

Marker

Chromosomal

defectsmono 6

15-25% ~60%~15%

b-catenin

stabilisation

mRNA

signature

17p loss (40%), 8p, 9q, 10q, 16q loss (all 30%), 7 gain,

MYC / MYCN amplification (each ~5%)

All FISH

Pathway activation SHH + SHH -

EpigeneticsCOL1A2 + COL1A2 -

Prognosis

Pathology desmoplastic

~50%~50%

Poor prognosisFavourable

prognosis

Non-

desmoplastic

Infant

medulloblastoma

(<3 yrs)

Biomarkers and Treatment

Individualisation

• SIOP / UKCCSG

• 1992-2000

• Pathology review and Biological studies - Newcastle

PNET3

S Clifford

1. Wnt/Wg sub-group tumours

S Clifford

b-catenin immunohistochemistry

& CTNNB1 / APC mutation analysis

109 cases

b-catenin nucleopositive MBs - 25%

CTNNB1 mutation in 60%

codon 32 GAC>TAC; ASP>TYR

codon 32 GAC>AAC; ASP>ASN

codon 32 GAC>TAC; ASP>VAL

codon 33 TCT>TAT; SER>TYR

codon 34 GGA>GAA; GLY>GLU

codon 37 TCT>TAT; SER>TYR

codon 37 TCT>TGT; SER>CYS

no APC mutation

b-catenin nucleonegative MBs - 75%

no CTNNB1 mutation

no APC mutation

S Clifford

Overall survival b-catenin nucleopositive vs.

b-catenin nucleonegative MBs

92% OS

65% OS

All nucleopositive M+ (n=4) or large cell/anaplastic (n=4) cases alive at 5 years

S Clifford

Wnt activation assessed by b-catenin

immunostaining (15% of cases)

WNT group: 7 average, 3 high-risk

‘Other’ group: 42 average, 17 high-risk

Event-free survival - overall

2. MYC family amplification

S Clifford

Clinical Trials Biological Studies

in Medulloblastoma

• Markers showing consistent findings in ≥2 clinical trials cohorts

• Others (chromosome 17, ERBB2, TRKC etc) not yet validated

Putative medulloblastoma disease

risk stratification 2010 (≥3yrs old)• Favourable risk (~15%)

b-catenin nucleopositive and

MYC / MYCN non-amplified and

M0 and

Classic or desmoplastic histology

• Standard risk (~55%)b-catenin nucleonegative and

MYC / MYCN non-amplified and

M0 and

Classic or desmoplastic histology

• High risk (~30%)MYC / MYCN amplified or

M+ or

Large cell / anaplastic histology

b-catenin nucleopositive or nucleonegative

• Identification of further markers, validation and refinement ongoing

S Clifford

SIOP PNET Clinical trials:

PNET5 & PNET6 – biological stratification

• Starting 2010/11

• Upfront biological and pathological testing:

• Newcastle – UK / European co-ordinating centre

• Mandatory submission of frozen tumour material for testing

• ‘Real-time’ biological assessment for treatment stratification

• PNET5 – favourable risk medulloblastoma

• Reduced therapy / late-effects?

• PNET6 – standard risk medulloblastoma

• Maintain survival rates?

PNET3

1992-2000

PNET4

2000-2007

PNET5/6

2010-

Feasibility

study

2009

Marker

Identification

Marker

validation &

refinement

New markers

& drug targets

Marker

selection

CCLG / SIOP PNET Clinical trials &

Biological studiesTrial Biological study

Surgery undertaken on cerebellar tumours

Local centre diagnosis of medulloblastomainc. M stage (cytology / radiology)

CCLG, Newcastle

Specimen preparation S Nicholson and BMS colleagues

Molecular diagnostics

N Bown,Regional Genetics,

Newcastle

CCLG NCL

Feedback Results to Local Centre

5 DAYSvia e-mail from NB to SLN.

3-5 DAYS

5-10 DAYS

3-5 DAYS CPR to SLN via e-mail

2 DAYS written proforma

Research

via. CCLG tumour bank

and approved studies

Frozen Tissue and FFPE routinely prepared locally

CCLG registration, despatch to NCL

Specified preparations all created

for study at one centre and

despatched to specific groups

22 day anticipated

turn-around for CPR

and Molecular

Diagnostics

Central Pathology ReviewK Robson, Nottingham

S Wharton, Sheffield

T Jacques, London

CCLG Feasibility Study: Strategy

PNET Clinical trials:

Future CCLG/SIOP biological studies in

Newcastle

• Refinement of favourable / average

risk medulloblastoma

• Infant medulloblastoma

• High-risk medulloblastoma

• Relapsed medulloblastoma

• sPNETs

S Clifford

Development of New Therapies

Summary:

Targeted therapies in medulloblastoma

Pathway activation Wnt/Wg SHH ???

Major mutational

targets CTNNB1 PTCH1 ???

Marker / PD

Chromosomal

defectsmono 6

15-25% ~60%~15%

b-catenin

stabilisation

SHH mRNA

signature

17p loss (40%), 8p, 9q, 10q, 16q loss (all 30%), 7 gain,

MYC / MYCN amplification (each ~5%)

S Clifford

Pre -clinical

Clinical Trial

No

No

Yes

PBTC/Genentech?

No (MYC)

No (MYC)

Cancer Cell. 6: 229-240, 2004.

• HhAntag691 (Curis/Genentech)

• Blocks SMO function (10x cyclopamine)

• Blood-brain penetration

• Assessment using PTCH (+/-) mouse MB modelS Clifford

Cancer Cell. 6: 229-240, 2004.

S Clifford

Delivery of agents targeting critical developmental

pathways to infants: potential issues

• SHH pathway activation more common in infant / desmoplastic tumours

Research Strategy

Clinical TrialsDevelopmental

Therapeutics

Exploratory Biology:

Biomarker and

Target Discovery

Translational research focused on improving

cancer therapy

Medulloblastoma outlook: 2010 on

Data from UKCCSG annual scientific review, 2005

??

?

2010 onwards

Group leader:

Steve Clifford

Clinical lead:

Simon Bailey (NHS)

Academic Clinical Lecturer:

Britta Vormoor

Lecturer in Neuro-oncology:

TBA (Faculty / JGWP)

Post-doctoral Scientists:

Janet Lindsey (SPARKS)

Meryl Lusher (SDBTT)

Matthew Allen (EU)

Biomedical Scientists:

Sarah Leigh Nicholson (CRUK / SDBTT)

Kieran o’Toole

Clinical Fellows:

James Hayden (CLIC / NECCR)

Chris Howell (JGWP / Action Research))

Becky Hill (CRUK / JGWP)

PhD students:Hisham Megahed (Egypt Govt.)

Ed Schwalbe (KT Trust / NECCR)

Dolores Hamilton (MRC)

Newcastle Children’s Cancer Research Group

NICR Drug Development & Pharmacology Programmes

(Boddy / Curtin / Newell)

Mouse modelling (Jackson / Lastowska / Bacon)

Newcastle Clinical Neuro-oncology Team (Oncologists /

Neuro-surgeons / Neuro-pathologists / Research Nurses)

Regional genetics service (Bown)

Kids Cancer Kinome and ITCC European consortia

UK Children’s Cancer and Leukaemia Group (CCLG)

SIOP PNET group

Cancer Genome Project, Sanger Centre (Futreal)

St. Jude Children’s Research Hospital

(Ellison / Gilbertson / Roussel)

AMC Amsterdam (Kool / Versteeg)

Team, funding &

major collaborations