Molecular Subtypes:Not Quite Ready for Prime Time

Scott Kopetz, MD, PhD. Department of GI Medical Oncology

MD Anderson Cancer Center

NOT YET

YES

Individual Biomarkers versus Molecular Subtypes

• Individual biomarkers:– Microsatellite instability in all patients

• For adjuvant decisions in Stage II and screening for HNPCC– KRAS, NRAS, BRAF in all metastatic patients

• For consideration of EGFR sensitivity and prognosis

• Molecular subtypes– 200 gene…400 gene…whole exome sequencing– Gene expression profiles– Proteomic panels

Why not yet….?

• We need studies to evaluate the benefit from extended molecular testing (beyond KRAS, NRAS, BRAF)

• We need to define the molecular subtypes by gene expression

• We need validated assays to move into the clinic

3

Why not yet….?

• We need studies to evaluate the benefit from extended molecular testing (beyond KRAS, NRAS, BRAF)

• We need to define the molecular subtypes by gene expression

• We need validated assays to move into the clinic

4

“My panel is bigger than yours…”

5

Integrating into Clinical Trials:Increase in Prospective Enrichment

Unen-riched

EGFR en-

riched

Novel enriched

13%

3%

Kopetz, et al JCO ‘08, updated from clinicaltrials.gov

Unen-riched

EGFR en-

riched

Novel enriched

9%

40%

2007-08 2011-12

Paucity of High-Frequency Targets Means Large Screening Efforts Needed

Currently “actionable”

Not actionableScreening size for a 20 patient

proof-of-principle study

100’s <3% frequency

Consent Tissue Acquisition

Block Selection, Extraction

Testing Completed

Results Relayed

Timeline for Biomarker Testing

6 calendar days28 calendar days

33 calendar days

Median Time:

ATTACC Program: Assessment of Targeted Therapies Against Colorectal

Cancer

• 5-FU refractory disease• ECOG PS 0-1• Tissue available for molecular testing

Eligibility

• Patients undergo biomarker assessment• CLIA-certified assaysScreening

• Based on biomarker, patients allocated to one of several treatment protocols

• Patients not expressing biomarker of interest are treated in unenriched protocols

Allocation

S. Kopetz, PI

CpG Island Methylation Demethylator Azacitadine + XELOXMitotic inhib Nab-paclitaxel

BRAF Mutation BRAF+EGFR+irino Vemurafenib +cetux+ irino

MD

Ande

rson

ATT

ACC

Prog

ram

: Bi

omar

ker S

cree

ning

for 5

-FU

Re

frac

tory

Met

asta

tic C

RCPTEN Loss or PIK3CAmut Akt inhibitor MK-2206

Exon 3,4 KRAS or NRAS mutant RAF inhibition LY3009120ERK inhibition Biomed Valley

HER2 overexpression HER2 inhibition Trastuzumab +/- EGFR HER2 mutation ERB family inhib TBA

Enrichment Therapeutic Agent(s)Mechanism

PTEN Loss/KRAS WT PI3K-beta inhibitor SAR26031

Aquired RAS mutation MEK + EGFR inhibition Panitum + Trametinib

EGFR ectodomain mutation Alternate EGFR Panitumumab

KRAS and PIK3CA mutation Dual MEK, PI3K BYL719 and MEK162

MSI High CTLA4 and PD1 Nivolumumab, Ipilumumb

Triple KRAS/BRAF/NRAS WT EGFR+HER2 Cetuximab + trastuzumab

N=550enrolled

Current Screening Panel

IonTorrent 50 gene panel

-IonProton 400 gene

CpG Methylation Panel

Immunohistochemistry

-PTEN, MET, HER2 expression

KRAS, NRAS, EGFR ectodomain mutation in

cfDNA/plasma

Microsatellite instability panel

42%

10%4%

20%

13%

2% 9%

Allocated to Study

Regorafenib

Poor PS/Death

Treatment at home

Treatment off protocol

Ineligibility

Withdrew consent

The Reality of Screening Studies1 in 5 Patients Allocation to Enrichment Study

Through 3/1/13, N=250, first new treatment on ATTACC

19% enriched companion study

Overall, 42% study enrollment, including 23% unenriched study

Practical Considerations for Enrichment Studies

• Enrichment strategies require…– Consenting patients for screening– Explaining the study– High research staff utilization per “screen failure”

• Patient-satisfaction is very dependent on biomarker turn-around time– Obtaining outside paraffin blocks is rate-limiting step– How long should one delay treatment waiting for a 5%

frequency biomarker? • Other experimental options need to be available

– Enrichment study is hard to justify to patients in isolation

Example: 19124802

BOTH

Pails

Kras

Braf

PIK3CAPTENAKT

WT/WT

STUDY DESIGN

DNA-based Screening Trial, based on NCI MATCH study

5-FU/Bev + drug A

Chemo + drug B

5-FU/Bev + drug C

5-FU/Bev + drug D

5-FU/Bev + drug E

FOLFOX/Bev x 8then

Maintenance

Endpoint PFSN = TBD but likely3000 – 5000Slide from P. O’Dwyer

ASSIGN Study:COLON CANCER TASK FORCE , NCI GI STEERING COMMITTEE

Flexibility & Centralization

Providing clinical data

Sending gDNA/cDNA

Sending Tumor tissue

Providing results

BIOBANKING

Centralizing and storing samplesExtracting gDNA/RNA

CLINICAL CENTERS

Treating and recruiting patients

EORTC Headquarters

Maintaining Sample Tracking tool, eCRF and results database

DIAGNOSTICS LABORATORIES

Performing BM analyses

Answering if patient eligible for study

Screening Effort ProtocolsEnrollmentSPECTAColorGoal: 600 pts/yearEnroll: 10-15% of screened

Slide from S. Tejpar

To date… Limited Prospective Biomarker Success in CRC

New or Anticipated Agents/Indications

– Bevacizumab (2nd line)– Ziv-aflibercept– Regorafenib– TAS-102

No new biomarker-directed therapy

Wrong premise, wrong implementation, or still too early?

Why not yet….?

• We need studies to evaluate the benefit from extended molecular testing (beyond KRAS, NRAS, BRAF)

• We need to define the molecular subtypes by gene expression

• We need validated assays to move into the clinic

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Two Approaches to Biomarker Integration

• Individual Biomarker Perspective– Biomarkers are paired with individual drugs

• Taxonomy Perspective– Move to a “Taxonomy” Perspective

Drug X Biomarker A

Drug X

Two Approaches to Biomarker Integration

• Individual Biomarker Perspective– Biomarkers are paired with individual drugs

• Taxonomy Perspective– Move to a “Taxonomy” Perspective

Drug X Biomarker A

Drug X

Definitions

Taxidermy = Stuffing Taxonomy = Grouping based on common patterns

CRC Taxonomy Hasn’t Been Defined To Date

Sotiriou et al NEJM, 2009; Alizadeh et al, Nature 2000

Bas

al

Lum

inal

A

Lum

inal

B

Her

2-po

s

?Breast Cancer Lymphoma Colorectal Cancer

Gene Expression Tests are “Fit for Purpose”

Prognostic Assays Taxonomy / Molecular Classification Assays

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0%5%

10%15%20%25%30%35%40%45%

0 10 20 30 40 50 60 70

3-ye

ar R

ecur

renc

e Ri

sk

Recurrence Score

≠

KRAS Poorly Recapitulates Taxonomy

Budinska et al ASCO ‘12

Stem-like (18%): MSS, Wnt high, crypt base, benefit CT and FOLFIRI, worse survival

MelbourneT:209 V:443128 genes

AgendiaT:188 V:54332/53/102 genes

FrenchT:443 V:105857 genes

AMC-AJCCII-90T:90 V:1074146 genes

PETACC3T:1113 V:72054 genes

TCGAT:220

Good prognosis (40%) Poor prognosis (60%): immune down/ cell signaling, ECM and focal adhesion pathways up

A-type (22%): BRAFm, MSI/dMMR, epithelial proliferative

A-type (62%): low mutation, MSS, epithelial proliferative, benefit adjuvant CT C-type (16%): mesenchymal, no benefit CT

CIN immune down (20%): conventional precursor

dMMR (20%): sessile serrated precursor, BRAFm, immune up

CSC (10%): serrated, poor survival

CIN Wnt up (30%): conventional precursor

CIN normal (10%): serrated, poor survival

KRASm (10%): serrated, CIMP+

CCS1 (50%): CIN+, KRASm and TP53m, left colon, Wnt high CCS2 (25%): MSI, CIMP+, BRAFm, right colon

CCS3 (25%): poorly dif, EMT, invasion, migration and TGF-β signaling, no benefit cetuximab

MSI/CIMP (30%): BRAFm, hypermutated

CIN (30%) Invasive (40%)

Surface crypt (26%): KRASm, EMT low, Wnt low, papillary or serrated phenotype

Lower crypt (30%): EMT low, Wnt high, tubular phenotype

Mesenchymal (19%): EMT/ CSC high Wnt low, poor prognosis, BRAFm, desmoplastic

CIMP+ (11%): MSI, BRAFm, immune up, mucinous

Mixed (14%): Wnt high, CSC high, tubular

SwissT:445 V:77430 genes

Goblet (14%): MSI, crypt top, Wnt low, no benefit adj CT, good prognosis

Inflammatory (18%): MSI, benefit FOLFIRI

Enterocyte (18%): crypt top ,Wnt low

TA cetux sensitive (18%): MSS, high EGFR ligands, good prognosis

TA cetux res (14%): MSS, stem cell, MET-inh sensitive, worse survival

Published Molecular Subtypes of Colorectal Cancer

Slide from Rodrigo Dienstmann

PIs: Justin Guinney Rodrigo Dienstmann

CLUSTER 2CLUSTER 3

CLUSTER 4

CLUSTER 1

Consensus clusters

ASCO 2014 Clinical Symposium: Colorectal Cancer: Not Just One Disease

Why not yet….?

• We need studies to evaluate the benefit from extended molecular testing (beyond KRAS, NRAS, BRAF)

• We need to define the molecular subtypes by gene expression

• We need validated assays to move into the clinic

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Development of Validated Assay is Nontrivial

28

“The same rigor that we use for development of the drug has to go into the biomarker development” R. Pazdur (FDA)

Conclusion

• Everyone should be testing for MSI and KRAS, NRAS, BRAF

• We need to do the studies to demonstrate benefit of more extended molecular profiling– Low yields for actionable mutations– Need more and better novel therapies

• A consensus is building for defining the subsets• The assays need to be built, and moved into

clinical labs.

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