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FGFR3-TACC3 Fusion FS 01Aug2016_v2.0

FGFR3-TACC3 Fusion

FactSheet

FGFR3-TACC3 Fusion FactSheet FGFR3-TACC3 fusion oncogenes are important targets for oncology research The fibroblast growth factor receptor (FGFR) family of tyrosine kinase receptors are involved in a wide range of cellular activities including proliferation, differentiation, and survival. Mutations, single nucleotide polymorphisms (SNPs), amplifications, and translocations of family members FGFR1 through FGFR4 have been implicated as causative factors in a variety of cancer types(1). Included within these translocations is the FGFR3 fusion with transforming acidic coiled-coil containing protein 3 (TACC3), which results in increased activation of FGFR3, fusion protein phosphorylation, MAPK pathway activation, nuclear localization, and cellular transformation(2). The FGFR3-TACC3 fusion has been identified at a low frequency in a range of different cancers including cervical cancer(3), 0.5%-2% of non-small cell lung cancers (NSCLC)(4), nasopharyngeal carcinoma(5), bladder cancer(6), and brain tumors(7). CrownBio FGFR3-TACC3 Fusion Resources

The functional capabilities of FGFR3-TACC3 fusion proteins are currently being investigated. Glioma, bladder, and lung cancer cells which express FGFR3-TACC3 fusion proteins, have been shown to be sensitive to FGFR tyrosine kinase inhibitors (TKIs)(8,9). Clinical trial treatment of a patient with cervical cancer carrying the FGFR3-TACC3 fusion with a multi-kinase TKI targeting FGFR also resulted in stable disease, suggesting FGFR inhibition(3). Recent research in head and neck squamous cell carcinoma xenograft models has shown that resistance to combined EGFR and ERBB3 blockade was driven by FGFR3-TACC3 fusion proteins via substituting for EGFR/RAS/ERK signaling. FGFR3-TACC3 fusions also promoted resistance to targeted therapy in cancer cell lines driven by EGFR signaling(9).

CrownBio has a range of ValidatedXeno™ cell line derived xenograft (CDX) and HuPrime® patient-derived xenograft (PDX) FGFR3-TACC3 fusion models for oncology research and drug development.

HuPrime PDX FGFR3-TACC3 Background and FGFR3 Status

Within the HuPrime collection, we have identified two PDX models harboring FGFR3-TACC3 fusions – the BN2289 glioma model and the LU6426 NSCLC squamous cell carcinoma model. The available patient background information, tumor pathology diagnosis, completed sequencing data, and mutational status of BN2289 and LU6246 are shown in Table 1. FGFR3 gene expression data for the two models is shown in Figure 1, and amplified DNA copy number for FGFR3 in the LU6426 model is detailed in Figure 2 (DNA copy number of 6).

Table 1: Summary of HuPrime FGFR3-TACC3 Fusion PDX Models hMSC: human mesenchymal stem cells

Patient Background

BN2289

Asian patient, aged 75 years

LU6426

Caucasian patient, aged 80 years, smoker USA

PDX Tumor Pathology QC

Genomic Profiling

Treatment History

Anaplastic oligodendrogliomas (WHO Grade 3). IHC results: GFAP(+), S-100(+), Syn(-), Ki-67(10% +), MMP-9(-), MGMT(-), P53(-), PCNA(+), P170(+)

Pa, P2: Oligodendrogliomas, Grade 3

P2: Affy U219 P1: Affy SNP 6.0 P5: RNAseq

NSCLC, SCC

P11: Poorly differentiated squamous cell carcinoma

P10: RNAseq

Tumor Pathology Diagnosis

UK

FRANCE

GERMANY

Models

CrownBio has the largest commercially available collection of approximately 2,500 PDX models. The HuPrime PDX collection closely reflects patient tumor histopathological profiles and is supported by a suite of curated patient and sample data including clinical diagnosis, patient clinical history, histopathology, mutational status, and genomic profiling. These data are collated in our free to access curated online PDX database, HuBase™, which can be accessed directly from the homepage of our website at www.crownbio.com.

These treatment responses and emerging data suggest that FGFR3-TACC3 fusions could provide ‘druggable’ targets for a selection of cancer patients, and could be the key to treating acquired drug resistance in certain cancer types. Appropriate preclinical models are now needed for evaluation of new agents, and for further research into the functional capabilities of FGFR3-TACC3 fusion.

HuPrime ID

Fusion

ITALY

CHINA

Mutation Status

Background & Model Type

Naive

WT: AKT, BRAF, CTNNB1, EGFR, KRAS, MAPK1, PIK3CA MYC amplified

BALB/c nude mice. Subcutaneous and orthotopic

Naive

WT: KRAS, LKB1, EGFR Mutation: TP53 R158L

MF-1 nude mice, hMSC supplement; BALB/c nude mice. Subcutaneous

JAPAN

AUSTRALIA

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NEW YORK SAN DIEGO SAN FRANCISCO

LONDON

PARIS

FRANKFURT

MILAN

SHANGHAI BEIJING

TOKYO

SYDNEY

Corporate Headquarters: Crown Bioscience Inc. 3375 Scott Blvd., Suite 108 Santa Clara, CA 95054 USA Tel: 855.827.6968 | Fax: 888.882.4881 [email protected] | www.crownbio.com

FactSheet HuPrime FGFR3-TACC3 Fusion Models Treatment Data

Figure 1: HuPrime FGFR3-TACC3 Fusion Models FGFR3 Gene Expression Data

Gene Expression (Log2(FPKM))

Gene expression levels of FGFR3 via RNAseq.

The standard of care (SoC) and experimental treatment data available for our PDX models with FGFR3-TACC3 fusions is shown in Table 2, with data acquired in BALB/c nude mice for the BN2289 model and MF-1 nude mice for LU6426.

9 8 7 6 5

Table 2: BN2289 and LU6426 SoC and Experimental Treatment Data

4 3 2 1 0

LU6426-P10

BN2289-P5

Model

Tumor Model

Figure 2: LU6246 DNA Copy Number Data Copy number calculated using custom FGFR (1-3) TaqMan® Copy Number Detection Kit (Applied Biosystems), passages 5 through 7 inclusive. RNase P used as an endogenous control. DNA Copy Number (Relative to RNase P)

8

6

Radiotherapy Resistant

4

2

0 FGFR2

The chromosome 4 position of the FGFR3-TACC3 fusion.

-

-

BGJ398 (FGFR inhibitor)

-

Temozolomide

LU6426 (MF-1 nude mice)

-

24Gy fractionated dose

-

AZD4547 (FGFR inhibitor)

Paclitaxel + carboplatin (acquired resistance)

Paclitaxel + carboplatin

*p≤0.001.

Chromosome

Junction Position

Strand

Downstream

Downstream

Fusion Gene Chromosome DownDownDownstream stream TACC3 4 stream Fusion ChromoStrand Gene some

HuPrime FGFR3-TACC3 Fusion Models Treatment Data

Downstream DownStrand

stream Genome + Junction Position

Downstream Genome Junction Position 1737000

The standard of care (SoC) and experimental treatment data available for our PDX models with BN2289 FGFR3 4 + 1808661 TACC3 4 + 1737000

INDIANAPOLIS LU6426 KANNAPOLIS (MF-1

nude mice)

Radiotherapy

-

Sensitive -

NEW YORK SAN DIEGO 24Gy SAN FRANCISCO

-

fractionated dose

GERMANY

Targeted Therapy

Chemotherapy

Resistant

Sensitive

Resistant

Sensitive

-

BGJ398 (FGFR inhibitor)

-

Temozolomide

LONDON

-

PARIS

AZD4547 (FGFR inhibitor)

Paclitaxel + carboplatin (acquired resistance)

FRANKFURT

Paclitaxel + carboplatin

. . . .

*

Study Day (Dosing Synchronized)

FGFR3-TACC3 fusions is shown in Table 2, with data acquired in Balb/c nude mice for the BN2289 model and MF-1 nude mice for LU6426.

Table 2: BN2289 and LU6426 SoC and Experimental Treatment Data USA UK FRANCE

. .

Mean Tumor Volume (mm3)



BN2289 (Balb/c nude mice) BOSTON

Sensitive

-

Comment [JB5]: Use image as is if it is high enough quality

Upstream Upstream Upstream Upstream Genome Fusion Strand Upstream Junction Chromosome UpGene Upstream UpPosition stream Genome Fusion stream FGFR3 4 + 1808661

Resistant

Chemotherapy Resistant

BN2289 (BALB/c nude mice)

Figure 3: HuPrime FGFR3-TACC3 Fusion PDX Model Genomic Profiling: LU6426 The chromosome 4 position of the FGFR3-TACC3 fusion.

Model

Sensitive

Figure 4: LU6246 PDX Model SoC Data Paclitaxel + Carboplatin: Response and Acquired Resistance

Figure 3: HuPrime FGFR3-TACC3 Fusion PDX Model Genomic Profiling: BN2289

Gene

Resistant

Standard of care chemotherapy agents have also been trialed with both of our FGFR3-TACC3 fusion models, appropriate for each specific disease type. The BN2289 model was sensitive to temozolomide, and the LU6426 model was sensitive to paclitaxel and carboplatin combination therapy. An LU6426 model of acquired resistance to paclitaxel and carboplatin has been developed through cycled dosing in vivo until a resistant phenotype emerged (Figure 4).

FGFR3

The FGFR3-TACC3 fusion has been confirmed in both models by RNAseq, and validated in the BN2289 model by PCR. Figure 3 exemplifies fusion data at exon 16 of the FGFR3 gene and exon 6 of the TACC3 gene on chromosome 4 for model BN2289. Further fusion data for both models are included within HuBase, and sequencing validation data are available on request.

PDX BN2289 model

Targeted Therapy

Sensitive

Radiotherapy can be used as an early stage treatment option for lung cancer, for patients who cannot or do not wish to have surgery, as well as a later stage option following surgery and/or combined with chemotherapy. LU6246 (admixed with hMSCs) showed tumor growth inhibition when treated with a 24Gy IR fractionated dose (3Gy q.d. x8). No adverse effects or adverse clinical signs were observed with this dose regimen. FGFR1

PDX model

FGFR3-TACC3 Fusion FS 01Aug2016_v2.0

FGFR3-TACC3 Fusion

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AUSTRALIA

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SHANGHAI BEIJING

TOKYO

SYDNEY

Corporate Headquarters: Crown Bioscience Inc. 3375 Scott Blvd., Suite 108 Santa Clara, CA 95054 USA Tel: 855.827.6968 | Fax: 888.882.4881 [email protected] | www.crownbio.com

FGFR3-TACC3 Fusion FS 01Aug2016_v2.0

FGFR3-TACC3 Fusion

FactSheet Figure 6: BN2289 PDX Model Response to FGFR Inhibitor BGJ398

Multi-targeted TKIs which inhibit a range of proteins including FGFR3 and other members of the FGFR family have also been trialed with these models. As expected, the LU6426 model was shown to be sensitive to AZD4547 an experimental FGFR1, 2, and 3 inhibitor which is currently in clinical trials for a range of FGFR expressing cancer types(10). The LU6426 model response to this treatment was also maintained in the acquired chemotherapy resistance setting (Figure 5).

1600

Vehicle q.d., p.o. BGJ398 15mg/kg q.d., p.o.

Tumor Volume (mm3)

1400

Figure 5: LU6426 PDX Model Response to FGFRi in Chemosensitive and Chemoresistant Settings A: Response to AZD4547 in LU6426 model sensitive to paclitaxel and carboplatin treatment. B: Response to AZD4547 in LU6426 model with acquired resistance to paclitaxel and carboplatin treatment. *p≤0.001.

1200 1000 800 600 400 200 0 0

Mean Tumor Volume (% Pre-Dose Volume)

A.

5

10

15

20

25

Study Days

ValidatedXeno RT112/84 CDX Model Background and FGFR3 Status

250

CrownBio has over 200 validated CDX models covering subcutaneous, orthotopic, and metastatic models. The ValidatedXeno CDX collection is well-characterized and validated, with all of the available model data (including gene expression and mutation analysis of up to 33 common oncogenes and tumor suppressor genes) stored in XenoBase® our free and easily searchable online cell line and CDX database. XenoBase can be accessed directly from the homepage of the CrownBio website at www.crownbio.com.

150

50

Study Day

Within the ValidatedXeno CDX collection is the RT112/84 bladder cancer model which, as previously published, contains the FGFR3-TACC3 fusion(11). The model type, model information, and background for RT112/84 are shown in Table 3.

B.

Tumor Volume (mm3)

1250

Table 3: Summary RT112/84 Model Background Model

750

RT112/84

Cancer Type

Model Type

Model Information

Background

Urinary tract; bladder

Subcutaneous, orthotopic, and bioluminescent

A human female epithelial bladder carcinoma, which is tumorigenic in nude mice. A clonal derivative of the RT112 cell line(12,13)

MF-1 female nude mice, NOD/SCID, BALB/c nude

250

RT112/84 Subcutaneous Model Treatment Data

Study Day

The SoC and experimental treatment data available for the subcutaneous RT112/84 model are summarized in Table 4, with data acquired using MF-1 female nude mice and BALB/c female nude mice.

The pan FGFR inhibitor BGJ398 was trialed in the BN2289 model, which also showed a robust response to this agent (Figure 6).

USA

UK

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GERMANY

ITALY

CHINA

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AUSTRALIA

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BOSTON INDIANAPOLIS KANNAPOLIS

NEW YORK SAN DIEGO SAN FRANCISCO

LONDON

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FRANKFURT

MILAN

SHANGHAI BEIJING

TOKYO

SYDNEY

Corporate Headquarters: Crown Bioscience Inc. 3375 Scott Blvd., Suite 108 Santa Clara, CA 95054 USA Tel: 855.827.6968 | Fax: 888.882.4881 [email protected] | www.crownbio.com

FactSheet Figure 8: RT112/84 Subcutaneous Model SoC Data Single Agent Docetaxel and Paclitaxel

Table 4: RT112/84 Single Agent SoC and Experimental Treatment Data Resistant

RT112/84 Subcutaneous

Sensitive

AZD4547 (FGFR inhibitor) resistant model being generated

T/C on Day 31: paclitaxel 105% (p=0.856); docetaxel 94% (p=0.843).

Chemotherapy Resistant

Lucitanib, lenvatinib, sunitinib. Regression/ stabilization with AZD4547 (FGFR inhibitor)

Sensitive

Docetaxel, paclitaxel

Partial response with cisplatin

Tumor Volume (mm3)

Targeted Therapy

Model

Cisplatin is currently used as a SoC therapy for bladder cancers which cannot be treated with surgery or radiotherapy, and the RT112/84 model showed a partial response following cisplatin treatment (Figure 7). Taxanes can be used for patients who cannot receive cisplatin, and the RT112/84 model has been shown to be resistant to treatment with both docetaxel and paclitaxel (Figure 8).

Mean Tumor Volume (mm3)

Mean Tumor Volume (mm3)

1000 800 600 400 200 0 5

10

15

20

25

30

Tumor Volume (mm3) Vehicle

1200

Cisplatin 4mg/kg

8

12

16

20

24

28

32

1600

Vehicle q.d. x 15, p.o. Sunitinib 40mg/kg q.d. x 30, p.o.

1200

Lucitanib 20mg/kg q.d. x 30, p.o. Lenvatinib 20mg/kg, q.d. x 30, p.o.

800

0

4

8

12

16

20

24

28

32

36

Days post Tumor Inoculation

800

Figure 10: RT112/84 Subcutaneous Model Single Agent AZD4547 (FGFR Inhibitor) Data

600 400

AZD4547 treatment initiated at tumor volume of 200mm3 in MF-1 female nude mice.

200

35

0

5

10

15

20 1200

25

Time (Days)

Mean Tumor Volume (mm3)

Mean Tumor Volume (mm3) 35

4

1000

Vehicle Cisplatin 4mg/kg

1000 800 600 400 200

30 35 Vehicle 10% Acacia q.d. p.o.

AZD4547 25mg/kg q.d. p.o.

1000 800 600 400 200 0

0 30

400

400

1400

25

800

2000

Time (Days)

1200

1200

2400

0 0

Paclitaxel 10 mg/kg Docetaxel 5 mg/kg

T/C on Day 31: sunitinib 24% (p