EML4-ALK: Oncogene Addiction Meets

Personalized Medicine

Thomas J Lynch, MDJonathan and Richard Sackler Professor of Internal Medicine

Director, Yale Cancer CenterPhysician-in-Chief, Smilow Cancer Hospital

Disclosure Slide

ConsultantBoehringer Ingelheim Pharmaceuticals Inc, Merck and Company Inc, SuperGen Inc

Stockholder Infinity Pharmaceuticals Inc

NCI SEER Cancer Statistics, WHO Fact Sheet

Lung Cancer 2011

• USA– 190,000 cases of lung cancer– 165,000 deaths– 165,300 cases of NSCLC– 115,000 cases of adenocarcinoma– 28,500 cases of lung cancer in never smokers

• Global– 1.4 million deaths from lung cancer

Cancer 2011

• Cancer is a disease caused by abnormal genes that “drive” either excessive cell growth or inadequate cell destruction

• Imbalance of growth and death signals leads to growth of cancer cells into tumors

• Tumors then proceed to grow and metastasize• Understanding which genes drive which cancers will

provide a “roadmap” to curing cancer

MacConall LE and Garraway LA. J Clin Oncol 2010;28:5219-28.

Major Classes of Genomic Alterations That Give Rise to Cancer• Point mutations• Copy number alterations

– Deletions– Amplifications

• Translocations– Examples: BCR-ABL, EML4-ALK

2011: Lung Adenocarcinoma —Multiple Molecular Subsets

Courtesy William Pao

Adeno

Squam

Large

Small

KRAS

Unknown

EGFR

HER2

BRAF

ALK fusionPIK3CA

MEK1

ROS fusionPDGFR amp

Adeno

Squam

Large

Small

KRAS

Unknown

EGFR

HER2

ALK fusion

2011: Never Smoker Lung Adenocarcinoma (US) — Almost All Molecular Subsets Defined!

Pham D et al. J Clin Oncol 2006;24(11):1700.Stephens P et al. Nature 2004;431(7008):525.Shaw AT et al. J Clin Oncol 2009;27(26):4247.Riely GJ et al. Clin Cancer Res 2008;14(18):5731.

With permission from Kwak EL et al. N Engl J Med 2010;363:1693-703. Copyright © 2010 Massachusetts Medical Society.

EML4-ALK Fusion Gene in NSCLC (Non-Small Cell Lung Cancer)

Soda M et al. Nature 2007;448;561.

Soda M et al. Nature 2007;448:561-567.

EML4-ALK Is a Potent “Oncogenic” Driver• Expression plasmids generated for wild-type EML4

and ALK, wild-type and mutant EML4-ALK, and v-Ras were introduced into mouse 3T3 fibroblasts.

• In vitro cell transformation and in vivo tumor formation in mice observed with only EML-4ALK, NPM-ALK or v-Ras expressing cells.

• Inhibition of ALK leads to dramatic in vivo tumor regression.

PIPPIP22

PLC-PLC-YY

IPIP33

MEKMEK

RASRAS

ErKErKS6KS6K

mTORmTOR

STAT3/5STAT3/5

BADBAD

PI3KPI3K

ALK Pathway

1. Inamura K et al. J Thorac Oncol 2008;3:13–17. 2. Soda M et al. Proc Natl Acad Sci USA 2008;105:19893–19897.

Figure based on: Chiarle R et al. Nat Rev Cancer 2008;8(1):11–23; Mossé YP et al. Clin Cancer Res 2009;15(18):5609–5614.

* Subcellular localization of the ALK fusion gene, while likely to occur inthe cytoplasm, is not confirmed.1,2

Translocation

Or

ALK ALK fusion protein*

Tumor cellproliferation

Inversion

Cell survival

AKTAKT

1 Shaw AT et al. J Clin Oncol 2009;27(26):4247-4253.With permission from Bang Y et al. Proc ASCO 2010;Abstract 3.

FISH = fluorescence in situ hybridization * Assay is positive if rearrangements can be detected in ≥15% of cells

FISH Assay for ALK Rearrangement*

Shaw AT et al. J Clin Oncol 2009;27(26):4247-53.

Clinical Features and Outcome of Patients withNon-Small Cell Lung Cancer Who Harbor EML4-ALK

• 141 pts screened for ALK fusions, 13% positive• M>F, young, non-smokers• No overlap between EGFR and Kras mutants• Refractory to EGFR TKIs• Typical chemo responses (not increased as with EGFR

mutations)• Signet ring cells are commonly found in

EML4-ALK-positive tumors

Alice T. Shaw, Beow Y. Yeap, Mari Mino-Kenudson, Subba R. Digumarthy, Daniel B. Costa, Rebecca S. Heist, Benjamin Solomon, Hannah Stubbs, Sonal Admane, Ultan McDermott, Jeffrey Settleman, Susumu Kobayashi, Eugene J. Mark, Scott J. Rodig, Lucian R. Chirieac, Eunice L. Kwak, Thomas J. Lynch, and A. John Iafrate

Shaw AT et al. J Clin Oncol 2009;27:4247–4253.

ALK(N = 12)

EGFR(N = 8)

WT/WT* (N = 34)

Response rate, % 25 50 35

TTP, months 9 10 8

Platinum-based chemotherapy

EGFR TKI

Patients with ALK-Positive NSCLC Do Not Appear to Respond to EGFR TKIs

ALK(N = 10)

EGFR

(N = 23)WT/WT* (N = 23)

Response rate, % 0 70 13

TTP, months 5 16 6

* WT/WT = wild type: no ALK fusion or EGFR mutation

Selectivity findings

• Crizotinib – ALK and c-MET inhibition at clinically relevant dose levels

• Crizotinib – low probability of pharmacologically relevant inhibition of any other kinase at clinically relevant dose levels

Cellular kinase selectivity of crizotinib

KinaseIC50 (nM)

mean Selectivity

ratio

c-MET 8 —

ALK 20 2X

RON298 34X

189 22X

Axl294 34X

322 37X

Tie-2 448 52X

Trk A 580 67X

Trk B 399 46X

Abl 1,159 166X

IRK 2,887 334X

Lck 2,741 283X

Sky >10,000 >1,000X

VEGFR2 >10,000 >1,000X

PDGFRß >10,000 >1,000X

Crizotinib (PF-02341066)

Crizotinib Selectivity Profile

13 kinase “hits” <100x selective for c-MET

Cohort 2 (n=4)

100 mg QD

Cohort 3 (n=8)

200 mg QD

Cohort 4 (n=7)

200 mg BID

Cohort 5 (n=6)

300 mg BID

Cohort 6 (n=9)

250 mg BIDMTD/RP2D

Part 2:Molecularly enriched cohorts

(ALK and c-MET)

Enrolling patients with ALK-positive NSCLC after preliminary observation of impressive activity in a few patients

• Data from database April 7, 2010• Data presented for 82 patients• Phase II target accrual (open): 400

Part 1:Dose escalation

Crizotinib: First-in-Human/Patient Trial

1 DLT: grade 3 ALTelevation

2 DLTs: grade 3 fatigue

Cohort 1 (n=3)

50 mg QD

ALT = alanine aminotransferase

With permission from Kwak EL et al. ASCO 2009;Abstract 3509.

Pre-treatment

After 2 cyclescrizotinib

Kwak EL et al. N Engl J Med 2010;363:1693-703. Copyright © 2010 Massachusetts Medical Society.

60

40

20

0

–20

–40

–60

–80

–100

Progressive disease

Stable disease

Confirmed partial response

Confirmed complete response

Max

imum

cha

nge

in tu

mor

siz

e (%

)

–30%

Tumor Responses to Crizotinib for Patients with ALK-positive NSCLC

*Partial response patients with 100% change have non-target disease present *

Kwak EL et al. N Engl J Med 2010;363:1693-703. Copyright © 2010 Massachusetts Medical Society.

Median PFS Has Not Been Reached 70% of Patients in Follow-up for PFS

1.00

0.75

0.50

0.25

0.00

Pro

gres

sion

-fre

e su

rviv

al p

roba

bilit

y

0 2.5 5.0 7.5 10.0 12.5 15.0 17.5Progression-free survival (months)

PFS probability at 6 months: 72% (95% CI: 61, 83%) 

Median follow-up for PFS: 6.4 months (25–75% percentile: 3.5–10 months) 95% Hall-Wellner confidence bands

Kwak EL et al. N Engl J Med 2010;363:1693-703. Copyright © 2010 Massachusetts Medical Society.

PFS

Current Crizotinib Clinical Trials

PROFILE 1007: NCT00932893; PROFILE 1005: NCT00932451

Key entry criteria

• Positive for ALK by central laboratory

• 1 prior chemotherapy (platinum-based)

N=318

PROFILE 1007

Crizotinib 250 mg BID (N=250)administered on a continuous

dosing schedule

Key entry criteria

• Positive for ALK by central laboratory

• Progressive disease in Arm B of study A8081007

• >1 prior chemotherapy

PROFILE 1005

RANDOMIZE

N=250

Crizotinib 250 mg BID (n=159)administered on a continuous

dosing schedule

Pemetrexed 500 mg/m2 ordocetaxel 75 mg/m2 (n=159)infused on day 1 of a 21-day cycle

Molecular Profiling

Kris MG et al.

Proc ASCO 2011;Abstract CRA7506.

Identification of Driver Mutations in Tumor Specimens from 1,000 Patients with Lung Adenocarcinoma: The Lung Cancer Mutation Consortium (LCMC)

Kris MG et al. Proc ASCO 2011;Abstract CRA7506.

Lung Cancer Mutation Consortium: Patients and Study Plan

Use data to selecttherapy

(erlotinib with EGFRmutation)

Recommended clinicaltrial of agent

specific for target

Report toLCMCvirtual

database

Mutational analysisCLIA-certified lab at LCMC site:

KRAS, EGFR, EML4-ALK, BRAF,HER2, PIK3CA, NRAS, MEK1,

AKT1, MET amplification Report tophysician

1,000 patientsStage IV

ECOG PS 0-2Lung adenocarcinoma

Sufficient tissue (paraffin)Informed consent

Centralconfirmation of

adenocarcinomadiagnosis(1 slide)

Lung Cancer Mutation Consortium:LCMC Protocols Linked to Specific Molecular Lesions Detected (I)

Target Agent(s) LCMC Lead

EGFRErlotinib + OSI 906Erlotinib + MM 121

C RudinL Sequist

KRASTivantinib + Erlotinib

GSK1120212J SchillerP Jänne

MET Amplification

EML4-ALK Crizotinib R Camidge

NRAS GSK1120212 P Jänne

Lung Cancer Mutation Consortium:LCMC Protocols Linked to Specific Molecular Lesions Detected (II)

Target Agent LCMC Lead

MEK1 GSK1120212 P Jänne

BRAF (V600E) GSK2118434 B Johnson

BRAF (not V600E) GSK1120212 P Jänne

HER2 Afatinib M Kris

PIK3CA BKM120 J Engelman

AKT1

Kris MG et al. Proc ASCO 2011;Abstract CRA7506.

Lung Cancer Mutation Consortium: Using LCMC Data to Guide Care – MSKCC Patients

121Enrolled

102Multiplex mutation testingand/or FISH completed

60 (59%)Driver mutations found

31 (30%)Received therapy

targeted tospecific mutation

19 – Erlotinib as initial therapy16 – Clinical trial of agent for identified mutation

Conclusions

• In 516 tumor samples analyzed by IHC and FISH, 54% were positive for a driver mutation.

• Mutational status information is being used in real time to select erlotinib as initial therapy and direct patients to linked trials.

Schema of personalized medicine.

Originally published by the American Society of Clinical Oncology. MacConaill LE, Garraway LA. J Clin Oncol 2010;28:5219-5228.

Genome Statistics

• 29,000 human genes

• Average gene 3,000 bases but wide variation exists

• 99.9% of our bases are exactly the same from person to person

• Functions are unknown for 50% of the discovered genes

Advances in massively parallel technologies have dramatically reduced the cost of sequencing

Originally published by the American Society of Clinical Oncology. MacConaill LE, Garraway LA. J Clin Oncol 2010;28:5219-5228.

Co

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ase

of

DN

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US

$) 100

101

0.10.01

0.0010.00011E-051E-061E-071E-081E-091E-10

1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025Years

US $/base pair

US $/IPS (Moore’s Law)

Progress in Sequencing the Human Genome

• 2000– 12 years– 1,800,000,000 USD

• 2010– 12 days– 20,000 USD

• 2011– 5 days– 5,000 USD

Yale Genome Statistics

• Human genome 3.2 billion bases or 3.2 Gbases

• September 2010 Yale sequences 1.8 trillion bases or 1,800 Gbases

• September 2010 Yale sequenced the equivalent of 562 human genomes!

• January 2011 Yale sequenced 1,300 human genomes!

• 2008: EGFR and Ras mutation testing routine

• 2009: Molecular genotyping — snapshot

• 2010: Whole genome sequencing begins experimentally

• 2012: Routine WGS available to patients

Will we be ready?

Post-Genome World