The Therapeutic Implications of EML4/ALK, ROS-1 and Other New Biomarkers

Lyudmila Bazhenova, MD Associate Clinical Professor Lung Cancer Unit Leader UC San Diego Moores Cancer Center

Objectives

• Review current state of targetable lung cancer biomarkers • Review and contrast clinical characteristics of patients with EML4-ALK, ROS 1, and KIFB5-RET fusion protein, testing strategies and agents with clinical activity.

Genomic Evolution of Lung Cancer

KRAS; 30% Unkn; 40% RET; 1% ROS1; 1% MEK; 1% PIK3CA; 1% FGFR4; 2% EML4-ALK; 5% HER 2; 2% BRAF; 2% EGFR; 15%

Mechanism of Action of ALK, ROS1 and RET Fusion Oncogenes

• All three are receptor tyrosine kinases (RTK) • ALK and RET are capable of homodimerization and self (ligant independend) activation • Mechanism of self activation of ROS1 is being debated • Downstream signaling via RAS/ERK (proliferation), and PI3K/AKT and JAK/STAT( resistance to apoptosis)

Testing for Fusion Oncogenes

IHC expression Amount of protein on the surface of the cell Break apart FISH F RT-PCR

ALK Fusion Gene

Echinoderm microtubule associated protein-like 4 N ?

anaplastic lymphoma kinase Adapted from Soda et al. Nature; 2007.

ALK Fusion Gene

C

Sasaki, European Journal of Cancer; 2010.

ALK Fusion Variants

Methods of ALK Detection

• • • FISH break apart – – Pros: independent of FPE Cons: if inversion involves a small locus of 2p it could be false negative; can not distinguish variants; cut of is 15% of nuclei with split signal; low throughput RT-PCR – – Pros: Rapid detection and identification of each unique variant Cons: False negatives; Loss of RNA during de parafinization; has to be multiplexed, i.e probes to all known variants. Unknown variants will not be detected. IHC – – Pros: easy Cons: several antibodies have been developed which look promising as a screening tool. No commercially available IHC in the US. • VENTANA just received an approval in China with 93% concordance with FISH, sensitivity 100%, specificity 98%

EML4-ALK Fusion

• • • • • Patients: younger, non smokers, with adenocarcinoma, adenosquamous carcinoma and rarely SCC Frequency: smokers 4% in all, 33% in EGFR negative never Biology: 16 EML4-ALK variants have been identified in NSCLC. Clinical significance of each variant is unknown.

Testing: Visys break apart FISH (> 15% cells with split signal in 50 nuclei scored). – ALK PCR, IHC Therapy: crizotinib 1 Shaw AT, ASCO; 2010; 2 Kris MG. ASCO 2011; abstract CRA7506.

3 Rodig SJ, Clin Cancer Res; 2009;15 Soda M, et al. Nature; 2007;448

Clinical Efficacy of Crizotinib

Some degree of tumor shrinkage 90% ORR - 60.8% DCR - 82.5% at week 8 Median time to response 7.9 weeks (2.1 - 39.6 weeks) Median response duration 49.1 weeks Median PFS 9.7 months (95% CI 7∙7–12∙8) N=149 Unknown… How crizotinib compares to chemotherapy 1 st • QOL • OS • TTP line Camidge, Lancet oncology 13, 2012

1

st

Line or Second Line

• • • • • No studies examining the best placement of the drug. FDA approved the drug without mentioning the line of therapy. One can make a leap of faith from EGFR inhibitors and use it in the first line.

Profile 1007 compared crizotinib to 2 nd – line chemotherapy PFS 7.7 m vs. 3 m in favor of crizotinib (HR 0.49; 95% CI, 0.37 to 0.64; P<0.001) – – RR 65% vs. 20 % in favor of crizotinib ( p<0.001) OS not different, 64% of patients in chemotherapy arm received crizotinib – QOL: greater reduction of symptoms and delay in new symptoms on crizotinib arm. Profile 1014 will compare crizotinib to 1 st line chemotherapy. Shaw NEJM ;June 2013

Shaw NEJM; June 2013.

PFS

Patient Related Outcomes

Shaw NEJM; June 2013

Characteristics of Progression

• Patients were allowed to stay on the study post progression if they continued to derive clinical benefi • Median duration of treatment 43.1 m (Range 0.1-136.8) • 69/149 patients had disease progression at the data cut off. – 39 continued to receive crizotinib for at least 2 weeks post progression • • 12 of them did that for 6 months Range of post progression treatment is 21 to 591 days. – Most common new sites of progression were brain ( N=10), lung (n=5), liver ( N=3) Camidge, Lancet oncology 13, 2012.

Duration of Initial Response and Post Progression Therapy

• • • • L1196M L1152R C1156Y F1174L

Crizotinib Resistance

Sasaki Clinical Cancer Research. Epub 2011.

Management of Crizotinib Resistance

• Local treatment with radiation for locally progressing disease – Clonal evolution • Platinum based doublet or triplet • Second generation ALK inhibitors – – – AP26114 LDK378 CH5424802 (RG7853) • HSP 90 inhibitors

Responses to Second Generation Inhibitors in crizotinib Resistant Tumors

• LDK378( phase I) 58% ORR 1 – CNS penetration • CH5424802 ( phase I/II) – – 48% ORR 2 CNS penetration • AP26113 ( phase I/II) – – 76% ORR 3 CNS penetration 1 Shaw. ASCO 2013 abstr 8010.

2 Gadgeel, World Lung 2013, O16.06.

3 Camidge. World Lung, MO0706

ROS1 Fusion

Oncogenic ROS1

• First described fusion gene FIG-ROS1 was found in glioblastoma – 240kb deletion on 6p21q resulting in a fusion gene coding for oncogenic fusion protein.

– Short and long isoforms – Induce tumorigenesis in xenograft mouse models • Also expressed in cholangiocarcinoma in 8.7% and ovarian cancer in 0.5%, gastric and colon, myofibroblastic tumors and angiosarcoma • EZR –ROS1 fusion gene has been shown to promote lung adenocarcinoma when ectopically expressed in lung epithelium Gu TL, PLoS One; 2011.

Birch AH, PLoS One; 2011; Lee, Cancer; May 2013 Bergethon et al.

JCO;

2012 (30)8.

Arai, PLOS ONE; February 2013.

ROS 1 Fusion Gene

ROS 1 Fusion Gene Variants

•

ROS1 Fusion

Patients: histology Younger, never smokers, adenocarcinoma, high grade • Frequency: 1.2 -1.7% in all • Biology: – 9 variants have been identified in NSCLC so far Clinical significance is unknown. Mechanism of activation is different. – FIG-, CD74-, SCL34A2-, TPM3-, SDC4-, EZR-, LRIG3, KDELR2 –, and CCDC6 – • Testing: nuclei scored) – Visys break apart FISH (> 15% cells with split signal in 50 ROS PCR, IHC • Therapy: crizotinib Shaw AT,

JCO

2012;30:(suppl; abstr 7508) Ou, Exp revi. of anticancer therapy 2012,;12 Gu TL, PLoS One. 2011; 6:e15640.

Birch AH, PLoS One. 2011; 6:e28250 Lee, Cancer May 2013 Davis Clin Cancer Res . Sep 2012 Bergeron, JCO, 30, 2012

Methods of ROS1 Detection

• RT-PCR – Cons: False negatives; 9 variants have been described in a matter of 12 months. Has to be multiplexed, i.e., probes to all known variants. Unknown variants will not be detected.

• FISH break apart – Cons: if inversion involves a small locus it could be false negative; can not distinguish variants; cut of is 15% of nuclei with split signal; low throughput • IHC – Cons: not commercially available, several antibodies appear promising

Response of a ROS1 Positive Patient to Crizotinib

• 49% homology in the TK domain and ATP binding site • Crizotinib is active in ROS1 fused cell cultures Baseline Bergeron, JCO, 30, 2012. 12 weeks

Clinical Validation of ROS1 as a Therapeutic Target

• 14 patients enrolled in phase I study • Safety/efficacy of crizotinib 250mg bid •

ROS1

rearrangement by FISH • Negative for

ALK

rearrangement • Average 54 yo, 13/14 never smokers • 80% received prior therapy • 8/14 responded (57%) Shaw et al.

JCO.

2012, 30 (suppl; abstr 7508.)

RET FUSION

Methods of RET Detection

• RT-PCR – Cons: False negatives; 3 variants have been described in a matter of 12 months. Has to be multiplexed, i.e probes to all known variants. Unknown variants will not be detected. • FISH break apart – Cons: if inversion involves a small locus it could be false negative; can not distinguish variants; cut of is 15% of nuclei with split signal; not widely available; low throughput • IHC – Current IHC antibodies do not correlate with RET fusion

RET Fusion Gene

RET Fusion

• Patients: AdenoCA and adenoSCC carcinoma, never or former smokers, poor differentiation ?, earlier LN metastases • Frequency: – 1.4% in all, – – 5.6 % in “triple negative”( EGFR, ALK, KRAS) 6.3% in non smokers negative for EGFR, KRAS, ALK, HER2, BRAF, and ROS1 – 16% in non smokers negative for EGFR, KRAS, ALK, ROS1, NRAS, BRAF, HER2, PIK3CA, MEK1, and AKT • Biology: – – 4 variants have been identified in NSCLC so far Clinical significance is unknown.

KIF5B-, CCDC6-, NCOA4-. TRIM33 Ju YS, Genome Res, 2012 Drilon, Cancer Discover March 2013 Wang R, J Clin Oncol 30: 2012 Kohno, Cancer Science Aug 2013

RET Fusion Gene

• Testing: Visys break apart FISH (> 15% cells with split signal in 50 nuclei scored) – RET PCR • Therapy: Unknown – – – Sunitinib, Sorafenib, Vandetanib, Carbozatinib, Ponatinib, and Lenvatinib all have potential for activity All active in KIF5B-RET –transformed cell lines Last 4 are in formal clinical trials

Clinical Activity of Carbozatinib in RET Fused Patients

4 weeks 4 weeks 4 weeks Drilon, Cancer Discover March 2013.

Summary

Discovery Type of the product Frequency Histology

ALK

2007 4% AdenoCA, AdenoSCC, SCC Other characteristics Approved agent Agent in consideration Crizotinib

ROS

2007 Receptor tyrosine kinase

RET

2012 1.7% AdenoCA Poorly differentiated Never smokers, younger 1.4% AdenoCA AdenoSCC Poorly differentiated?

None Crizotinib None Sunitinib Sorafenib Carbozatinib Vandetanib Ponatinib Lenvatinib

HER 2 Insertions

•

Patients:

Adenocarcinomas, never smokers •

Frequency:

Incidence 2.8-4.2% •

Biology:

– In-frame insertions into exon 20. Transgenic mouse models confirm oncogenicity •

Therapy:

– Drugs of interest: neratinib, afatinib, dacomitinib • • • Preclinical models show synergy with mTOR inhibitors. Clinical trial of neratinib + temsirolimus ongoing, several PR are reported Both afatinib and dacomitinib have case reports of responses

BRAF Mutations

•

Patients: smokers and non smokers

•

Frequency:

1.6-3% •

Biology:

majority of the mutations are non V600E (more likely in smokers), V600E ( more likely in never smokers) •

Therapy:

– One case report or a NSCLC patient with V600E patient responding to vemurafenib – – Dabrafenib is being tested in patients with V600E NSCLC MEK inhibitors are being considered for non V600E patients

Q&A