Oncogenic Mechanisms and Prevalence of FGFR3-BAIAP2L1

Author Manuscript Published OnlineFirst on January 14, 2015; DOI: 10.1158/1535-7163.MCT-14-0927-T Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Mechanism of oncogenic signal activation by the novel fusion kinase FGFR3-BAIAP2L1

Yoshito Nakanishi, Nukinori Akiyama, Toshiyuki Tsukaguchi, Toshihiko Fujii, Yasuko

Satoh, Nobuya Ishii, and Masahiro Aoki

Authors' Affiliation: Research Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara,

Kamakura, Kanagawa 247-8530, Japan

Note: Y. Nakanishi and N. Akiyama are co-first authors who contributed equally to this study.

Running Title: Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Keywords: FGFR3-BAIAP2L1, BAR domain, CH5183284/ Debio 1347, FGFR inhibitor, oncogene

Downloaded from mct.aacrjournals.org on October 2, 2021. © 2015 American Association for Cancer Research. Author Manuscript Published OnlineFirst on January 14, 2015; DOI: 10.1158/1535-7163.MCT-14-0927-T Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Financial/grant information: None

Corresponding Author: Yoshito Nakanishi, Research Division, Chugai Pharmaceutical Co.,

Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan. Phone: 81-467-47-6262; Fax:

81-467-46-5320; E-mail: [email protected]

Disclosure of Potential Conflicts of Interest: All authors are employees of Chugai

Pharmaceutical Co., Ltd. The company was involved in the data analysis and the decision to

publish this manuscript.

Word count (from beginning of Introduction to the end of Discussion): 3518 words

Word count (Abstract): 223 words

Total number of figures and tables: 7 (5 figures, 2 table)

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Abstract

Recent cancer genome profiling studies have identified many novel genetic

alterations, including rearrangements of genes encoding fibroblast growth factor receptor

(FGFR) family members. However, most fusion genes are not functionally characterized, and

their potentials in targeted therapy are unclear. We investigated a recently discovered gene

fusion between FGFR3 and BAI1-associated protein 2-like 1 (BAIAP2L1). We identified 4

bladder cancer patients and 2 lung cancer patients harboring the FGFR3-BAIAP2L1 fusion

through PCR and fluorescence in situ hybridization assay screens. To investigate the

oncogenic potential of the fusion gene, we established an FGFR3-BAIAP2L1 transfectant

with Rat-2 fibroblast cells (Rat-2_F3-B). The FGFR3-BAIAP2L1 fusion had transforming

activity in Rat2 cells, and Rat-2_F3-B cells were highly tumorigenic in mice. Rat-2_F3-B

cells showed in vitro and in vivo sensitivity the selective FGFR inhibitor CH5183284/Debio

1347, indicating that FGFR3 kinase activity is critical for tumorigenesis. Gene signature

analysis revealed that FGFR3-BAIAP2L1 activates growth signals, such as the

mitogen-activated protein kinase pathway, and inhibits tumor-suppressive signals, such as the p53, RB1, and CDKN2A pathways. We also established Rat-2_F3-B-ΔBAR cells expressing

an FGFR3-BAIAP2L1 variant lacking the Bin–Amphiphysin–Rvs (BAR) dimerization

domain of BAIAP2L1, which exhibited decreased tumorigenic activity, FGFR3

phosphorylation, and F3-B-ΔBAR dimerization, compared to Rat-2_F3-B cells. Collectively,

these data suggest that constitutive dimerization though the BAR domain promotes

constitutive FGFR3 kinase activation and is essential for its potent oncogenic activity.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Introduction

Chromosomal translocations/rearrangements are major drivers of tumorigenesis.

Since the discovery of the BCR-ABL gene fusion in chronic myeloid leukemia, several fusion

kinases have been identified in hematological and epithelial malignancies, including

anaplastic lymphoma kinase (ALK) fusions, RET fusions, and ROS1 fusions (1-3). Generally, the partner proteins of fusion kinases possess dimerization domains, which promote kinase domain dimerization and constitutive activation. Several small molecule inhibitors have been developed to treat cancer patients with oncogenic fusion kinases. For instance, the ALK inhibitors crizotinib or alectinib have demonstrated excellent targeted activity against cancers harboring EML4-ALK gene fusions (4, 5).

Normally, the fibroblast growth factor receptor (FGFR) receptor tyrosine kinase is

transiently activated FGF ligand-mediated homo/heterodimerization. The FGFR signaling

pathway is constitutively activated by genetic alterations such as gene amplifications, point

mutations, or chromosomal translocations/rearrangements, which promote cell growth, angiogenesis, cell migration, invasion, and metastasis (6). FGFR1 amplification is a key genetic alteration in squamous cell lung carcinoma and hormone receptor-positive breast cancer (7, 8), whereas FGFR2 is amplified in gastric cancer (9). FGFR2 and FGFR3 point mutations are mainly observed in endometrial cancer and bladder cancer, respectively (10,

11). Since the first reports of FGFR1 and FGFR3 fusion genes in hematological malignancies

(12, 13), several novel chromosomal translocations/rearrangements of FGFRs have been

discovered in glioblastoma, bladder cancer, breast cancer, and cholangiocarcinoma patients

by next-generation sequencing (NGS) technology (14-17).

A well-characterized gene fusion occurs between FGFR3 and the transforming

acidic coiled-coil containing protein 3 (TACC3) gene. TACC3 contains a coiled-coil domain

and exerts ligand-independent activation upon dimerization (17). The constitutively activated

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

FGFR3-TACC3 protein can promote ERK and STAT3 signaling (16, 18). miR-99a targets the

3-untranslated region (UTR) of FGFR3 to suppress FGFR3 expression in normal tissues.

However, because the FGFR3 fusion loses its 3-UTR, the fusion protein is highly expressed

(19).

The FGFR3-BAI1-associated protein 2-like 1 (BAIAP2L1) fusion gene has not been

identified in clinical tumor samples. Although FGFR3-BAIAP2L1 dimerization and increased

ERK and STAT1 phosphorylation in FGFR3-BAIAP2L1-positive cells has been reported (18),

the mechanism of constitutive activation and associated signaling pathways are unclear.

Therefore, we assessed the prevalence of the FGFR3-BAIAP2L1 fusion gene in clinical samples, studied its tumorigenic activity in vitro and in vivo, and investigated its signaling pathway. BAIAP2L1 has a Bin–Amphiphysin–Rvs (BAR) domain, which is the most conserved feature in amphiphysins. The BAR domain forms a crescent-shaped dimer that preferentially binds highly curved, negatively charged membranes (20). In the

FGFR3-BAIAP2L1 fusion, the BAIAP2L1 fragment, including the BAR domain, is fused

with the C-terminal domain of FGFR3, and therefore FGFR3-BAIAP2L1 retains the entire

kinase domain of FGFR3. To clarify the role of BAR domain in the FGFR3-BAIAP2L1

fusion kinase, we compared the tumorigenic and dimerization activities of

FGFR3-BAIAP2L1 and FGFR3-BAIAP2L1 lacking the BAR domain.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Materials and Methods

Reagents and cell lines

A 1-(1H-benzimidazol-5-yl)-5-aminopyrazole derivative, CH5183284/Debio 1347,

was synthesized at Chugai Pharmaceutical Co. Ltd., as described in the publication (21).

SW780, RT4, 3T3, 293, HT1376, and HCT116 were purchased from the American Type

Culture Collection, Rat-2 was purchased from the Health Science Research Resources Bank,

and RT112/84 is purchased from Health Protection Agency Culture Collections. All Cell lines

were obtained more than one year ago from each experiment and were propagated for less than 6 months after thawing and cultured according to suppliers’ instructions.

PCR, Sanger sequencing of FGFR3-BAIAP2L1 gene fusions and Break-apart fluorescence in situ hybridization (FISH) assays

Sequencing of clinical samples was conducted under IRB-approved protocols

conducted at Chugai Pharmaceutical Co., Ltd. cDNAs from clinical samples derived from

patients with bladder cancer (n = 46), lung cancer (n = 83), head and neck cancer (n = 17),

and gastroesophageal cancer (n = 18) were obtained from OriGene Technologies, Inc. or

TriStar Technology Group, LLC. The information of primers of PCR is available in

Supplemental Material and Methods. For FGFR3 break-apart FISH experiments, 4-µm thick formalin-fixed, paraffin-embedded sections were deparaffinized and treated with

Pretreatment Reagent (Abbott) for 10 min at 95°C. Pepsin solution (ZytoVision) was added and samples were incubated at 37°C for 10 min. FGFR3 gene rearrangements were detected with the FGFR3 Split Dual Color FISH probe (GSP Lab., Inc.). Slides and probes were denatured simultaneously at 75°C for 10 min, followed by hybridization at 37°C overnight with ThermoBrite® (Abbott Molecular, Inc.). Slides were washed with 0.3% NP-40/2x SSC at 72°C for 2 min and stained with DAPI (Life Technologies).

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Colony formation assays, spheroid formation assays and xenograft transplantation

studies

Rat-2 cells were infected with lentiviruses, and stable transductants were selected in

puromycin (1 µg/mL medium). Colony formation activities of stably transduced Rat-2 cells

were measured with CytoSelectTM 96-Well Cell Transormation assay kit (CELL BIOLABS,

INC.). Stably transduced Rat-2 cells were seeded in 6-well or spheroid plates (Sumilon

Celltight Spheroid 96U; Sumitomo Bakelite, Inc.) and incubated for 3–4 days at 37°C. Cell

morphologies were observed microscopically, and cell viabilities were measured using the

CellTiter-Glo® Luminescent Cell Viability Assay Kit (Promega). Female BALB -nu/nu mice

(CAnN.Cg-Foxn1/CrlCrlj nu/nu) were obtained from Charles River Laboratories Japan

and housed under specific pathogen-free conditions. Stably transduced Rat-2 cells were

suspended in serum-free medium and 5  106 cells were injected subcutaneously into the right

flanks of 7–9-week-old mice. Tumors were measured using a gauge twice weekly, and tumor

volumes (TVs) were calculated as: TV = a  b2/2, where a is the tumor length, and b is the width (22). All in vivo studies were approved by the Chugai Institutional Animal Care and

Use Committee.

In vitro and in vivo efficacy studies

Cell lines were seeded in 96-well plates (Sumilon Celltight Spheroid 96U) in medium containing final CH5183284/Debio 1347 concentrations of 0.003–20,000 nM and

incubated at 37°C for 4 days. Subsequently, cell viabilities were measured using the

CellTiter-Glo® Luminescent Cell Viability Assay Kit. For in vivo efficacy studies, cells were

implanted into mice as described above. After tumors reached ~200–300 mm3, animals were randomized into groups (4–5/group), and received oral CH5183284/Debio 1347

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

administration once/day.

Western blot analysis

Cells were treated with CH5183284/Debio 1347 or a solvent control (0.1% dimethyl

sulfoxide; DMSO) for 2 h and lysed in Cell Lysis Buffer (Cell Signaling Technology)

containing protease and phosphatase inhibitors. For animal studies, xenograft tumors were

homogenized using a BioMasher (K.K. Ashisuto) before lysis. Cell lysates were denatured

with Sample Buffer Solution with Reducing Reagent for SDS-PAGE (Life Technologies) and

resolved on precast 10% or 5–20% SDS-PAGE gels (Wako Pure Chemical Industries, Ltd.).

After electroblotting, western blot analysis was performed as described (23). Antibody references are available in Supplemental Material and Methods.

RNA-Seq and expression analysis

Cellular RNA was extracted using the RNeasy Mini Kit (Qiagen, Inc.). Quality

assessment, poly-A selection, and sequencing with a HiSeq 2000 Sequencing System

(Illumina) were performed by Macrogen, Inc. Cellular RNA samples were prepared for

sequencing using a TruSeq RNA Sample Preparation Kit (Illumina) to generate an mRNA

library, and 100 bases were sequenced from both ends of the library. RSEM software was

used to align reads against RefSeq transcripts and calculate expression values for each gene

(24). Fold-changes in expression levels were calculated to identify downregulated genes

(<80% expression) and upregulated genes (>120% expression), relative to Rat-2_mock cells

and other cell lines. We also purified and sequenced total RNA from Rat-2_F3-B cells treated

for 24 h with either 0.1% DMSO or 1 µM CH5183284/Debio 1347. Fold-changes were calculated by normalizing gene expression levels in CH5183284/Debio 1347-treated cells to

DMSO control cells, identifying suppressed (< 50% expression) or induced genes (>200%

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

expression), relative to DMSO controls.

Phosphorylation levels and dimerization activities of FGFR3 constructs

cDNAs encoding WT FGFR3, F3-B, F3-B-BAR, BAIAP2L1, F3-B lacking the SH domain (aa 342–401; F3-B-SH), F3-B lacking the SH and BAR domains

(F3-B-BAR/SH), and kinase dead (K508M) F3-B (F3-B-KD) were inserted into the

pCXND3 vector (Kaketsuken) and used to transfect 293 cells. At 72 h post-transfection, cells

were lysed in Cell Lysis Buffer (Cell Signaling Technology). Lysates were then studied by

western blot analysis. In separate experiments, 293 cells were transfected with the

FLAG-tagged or Myc-tagged expression construct alone or in combination, using the FuGene

HD reagent (Promega). At 3 days post-transfection, cells were lysed and immunoprecipitation

was performed with Anti-FLAG M2 Affinity Gel (Sigma-Aldrich). Precipitates were washed

10 times with Cell Lysis Buffer and eluted at 95°C for 5 min with Reducing Reagent for

SDS-PAGE (Life Technologies).

Results

Identification of patients harboring FGFR3 rearrangements

Although the FGFR3-BAIAP2L1 fusion gene was identified in a cell line (17), it has

not yet been discovered in clinical tumor samples. Therefore, we established PCR and

break-apart FISH assays to screen clinical samples for the FGFR3-BAIAP2L1 gene fusion.

We detected the FGFR3-BAIAP2L1 fusion by PCR in 1 out of 28 lung adenocarcinoma

patients, 1 out of 28 squamous cell lung carcinoma patients, and 2 out of 46 bladder cancer

patients (Table 1) and confirmed the junction sequences by Sanger sequencing (Fig. 1A). The clinico-pathologic characteristics are available (Supplementary Table S1) and so far, there

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

was no clear association with FGFR fusions. While the proximity of FGFR3 and TACC3 in

the human genome is too close to discern FGFR3-TACC3 gene fusions in break-apart assays

(Approximately 70 kb, Supplementary Fig. S1), we could detect split FGFR3 signals in

SW780 cells harboring the FGFR3-BAIAP2L1 rearrangement (t(4;7), Fig. 1B). Thus, we

performed a prevalence study for FGFR3-BAIAP2L1 rearrangements in bladder cancer specimens and found that 2 out of 89 bladder cancer patients harbored this rearrangement

(Fig. 1C).

Oncogenic activity of the FGFR3-BAIAP2L1 fusion kinase in normal rat fibroblast cells

To determine whether the F3-B fusion promotes oncogenic activity, we generated

Rat-2 cell line clones stably transduced with an empty lentiviral vector (Rat-2_mock), or lentiviral vectors expressing FGFR3 (Rat-2_FGFR3), F3-B (Rat-2_F3-B), or BAIAP2L1

(Rat-2_BAIAP2L1). Consistent with previous reports (17, 18), we observed a spindle-type cellular morphology in Rat-2_F3-B cells, but not in other transductants (Supplementary Fig.

S2A). We also observed ligand-independent FGFR3-BAIAP2L1 phosphorylation in

Rat-2_F3-B cells (Supplementary Fig. S2B). Furthermore, Rat-2_F3-B cells showed an

anchorage-independent growth in a soft agar assay and in a spheroid formation assay (Fig.

2A, 2B). FGFR3-BAIAP2L1 expressing 3T3 cells showed similar behaviors in several assays

(Supplementary Fig. S2C, S2D, S2E). To evaluate the tumorigenic potential of the gene

fusion in mice, we inoculated nude mice with Rat-2_mock, Rat-2_FGFR3, Rat-2_F3-B, and

Rat-2_BAIAP2L1 cells and measured tumor sizes at 15 days post-inoculation. The

Rat-2_F3-B cells formed large tumors (>1 000 mm3), while the other cell lines formed small

tumors (<100 mm3; Fig. 2C). To demonstrate that kinase activity is essential for the

oncogenic activity of FGFR3-BAIAP2L1, we evaluated the anti-proliferative activity of

CH5183284/Debio 1347, a selective FGFR inhibitor, in spheroid cultures. CH5183284/Debio

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

1347 showed anti-proliferative activity against FGFR3-BAIAP2L1-positive cells only, including the bladder cancer cell line SW780, Rat-2_F3-B cells, and NIH-3T3 cells expressing FGFR3-BAIAP2L1 (3T3_F3-B), but not against NIH-3T3 cells expressing

EML4-ALK (3T3_EML4-ALK) or HT1376 cells harboring wild-type FGFR (Fig. 2D). Other

structurally distinct FGFR inhibitors also inhibited cell proliferation of SW780 or

Rat-2_F3-B cells (Supplementary Table S2). Furthermore, CH5183284/Debio 1347 induced

apoptosis in SW780 and Rat-2_F3-B cells (Supplementary Fig. S3A) and suppressed FRS

and ERK phosphorylation (Fig. 2E). CH5183284/Debio 1347 showed in vivo anti-tumor

activity in SW780 and Rat-2_F3-B xenograft models, but not in wild-type FGFR HT1376

xenograft tumors (Fig. 2F). The downstream signals were suppressed in Rat-2_F3-B

xenograft tumors treated by CH5183284/Debio 1347 (Fig. 2G). We also found that siRNAs

targeting the FGFR3, BAIAP2L1, and FGFR3-BAIAP2L1 fusion transcripts showed

anti-proliferative activities against SW780 cells (Supplementary Fig. S3B, S3C). Collectively,

these data demonstrated that the FGFR3-BAIAP2L1 fusion kinase promoted tumor growth in

vivo and that its kinase activity was important for oncogenic activity.

Downregulation of tumor-suppressive pathways by the FGFR3-BAIAP2L1 fusion kinase

A previous study reported that the FGFR3-BAIAP2L1 fusion kinase induced ERK

and STAT1 phosphorylation (18); however, the mechanisms of tumor growth promotion in

vivo by FGFR3-BAIAP2L1 have not been demonstrated. Therefore, we conducted a

comprehensive gene expression analysis by NGS using 4 cell lines (Rat-2_mock,

Rat-2_FGFR3, Rat-2_F3-B, and Rat-2_BAIAP2L1). These cell lines were cultured under

normal growth conditions and total RNAs were prepared for RNA-Seq with an Illumina

HiSeq2000. We identified 1,566 upregulated genes and 1,916 downregulated genes in

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Rat-2_F3-B cells, compared with expression levels observed in Rat-2_mock cells or

Rat-2_FGFR3 cells (Fig. 3A). To select genes that are regulated by FGFR3 kinase, we

identified a subset of genes whose differential expression levels were reversed by

CH5183284/Debio 1347 treatment (Supplementary Fig. S4). Finally, we selected 210 genes

comprising an FGFR3-BAIAP2L1-regulated gene signature (Supplementary Table S3), which was analyzed by Ingenuity Pathway Analysis (IPA) software (Ingenuity® Systems) to identify upstream regulators. The results indicated that the RB1, p53, and p16 pathways were suppressed in Rat-2 cells expressing FGFR3-BAIAP2L1, while the E2F2 and E2F1 pathways

were activated (Table 2). To confirm that these pathways are similarly regulated in vivo,

xenograft tumors from mice implanted with Rat-2_mock, Rat-2_FGFR3, Rat-2_F3-B, and

Rat-2_BAIAP2L1 cells were analyzed by western blot (Fig. 3B). As previously reported (18),

phospho-ERK and phospho-MEK were upregulated only in Rat-2_F3-B tumors. Cyclin D1

protein levels were elevated because of mitogen-activated kinase (MAPK) pathway activation,

whereas phospho-AKT was downregulated. Consistent with the IPA results, p53 and p21 expression were markedly decreased. Similarly, decreased phosphorylation of RB1 and p27

was observed in Rat-2_F3-B-derived xenograft tumors. Collectively, these results suggested

that FGFR3-BAIAP2L1 activated the MAPK pathway and downregulated tumor-suppressive

pathways involving RB, p53, and CDKN2A.

The FGFR3-BAIAP2L1 fusion kinase BAR domain is essential for oncogenic activity

Most partner genes of fusion kinases have dimerization motifs such as coiled-coil

domains, and kinase domain dimerization can lead to constitutive kinase domain activation

(25). The BAR domain of BAIAP2L1 contains a known dimerization motif, but it is uncertain

if the BAR domain facilitates dimerization or promotes oncogenic activity through

constitutive kinase activation. To study BAR domain function in FGFR3-BAIAP2L1, we

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

established Rat-2 cells expressing FGFR3-BAIAP2L1 without the BAR domain

(Rat-2_F3-B-BAR, Fig. 4A) and compared its oncogenic potential with that observed with

Rat-2_F3-B cells. We first measured the spheroid formation capacity of Rat-2_F3-B-BAR

cells relative to those of Rat-2, Rat-2_mock, Rat-2_FGFR3, and Rat-2_F3-B cells.

Rat-2_F3-B-BAR formed 1.4-fold more spheroids than Rat-2_mock cells, whereas

Rat-2_F3-B formed 26-fold higher spheroids (Fig. 4B). Next, we evaluated tumorigenesis of

Rat-2_F3-B cells in nude mice. Xenograft tumors derived from Rat-2_F3-B cells formed large tumors (average size: 1,600 mm3) by 14 days post-tumor implantation (Fig. 4C).

However, Rat-2_F3-B-BAR cells formed tumors that were >10-fold smaller (average size:

89 mm3). We confirmed that the FGFR3 constructs were expressed approximately equally in

each cell line (Supplementary Fig. S5). The observations that the spheroid forming activities

of Rat-2_F3-B and Rat-2_F3-B-BAR cells were essentially the same in the presence of

FGF1 ligand (Fig. 4D) and that FGF1 induced F3-B-BAR phosphorylation (Supplementary

Fig. S6) both suggested that differences in tumorigenic activity without FGF1 were not due to

conformational alterations of the fusion proteins that affected kinase activity, but were solely dependent on BAR domain function. These data demonstrated that the BAR domain of

FGFR3-BAIAP2L1 was essential for the observed oncogenic activity.

Contribution of the FGFR3-BAIAP2L1 fusion kinase BAR domain to dimerization

activity

To study the requirement of the FGFR3-BAIAP2L1 BAR domain for oncogenic activity, we examined activation statuses with a FGFR3 deletion series in Rat-2 cells. 293 cells were transfected with the empty pCXND3 vector, or pCXND3 constructs encoding

FGFR3, F3-B, F3-B-ΔBAR, F3-B with the SH domain deleted (F3-B-ΔSH), F3-B with the

BAR and SH3 domains deleted (F3-B-ΔBAR/ΔSH), and kinase dead F3-B (F3-B-KD) (Fig.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

5A). Next, FGFR3 phosphorylation in transfectants was analyzed in western blots (Fig. 5B).

Compared with FGFR3, F3-B phosphorylation was markedly increased, and no phosphorylation of the kinase dead mutant (K508M) was detected, suggesting that FGFR3 phosphorylation results from auto-phosphorylation. Among the F3-B deletion mutants

studied, FGFR3 phosphorylation in cells expressing the F3-B-ΔBAR and F3-B-ΔBAR/ΔSH

variants was remarkably diminished. Then, we validated FGFR3 dimerization in 293 cells

transfected with FLAG-tagged and/or Myc-tagged FGFR3 fusion variants by

immunoprecipitation of FLAG tagged proteins (Fig. 5C). Although the Myc-tagged F3-B was co-immunoprecipitated with FLAG-tagged F3-B, we only detected a minor portion of

co-immunoprecipitated Myc-tagged F3-B-ΔBAR with FLAG-tagged F3-B-ΔBAR. These

data indicated that the FGFR3-BAIAP2L1 protein dimerizes through the BAR domain to

facilitate constitutive FGFR3 kinase domain activation.

Discussion

Although a comprehensive landscape of molecular alterations associated with cancer

was provided by The Cancer Genome Atlas Project and by other groups, FGFR3-BAIAP2L1

rearrangements have not been previously discovered in clinical tumor samples (8, 15, 26, 27).

The lack of reports documenting oncogenic FGFR3-BAIAP2L1 rearrangements may relate to

the detection methods used. By using an FGFR3-BAIAP2L1-specific PCR assay, we attained higher sensitivity than expected with NGS technology. Currently, the number of novel genes

implicated in tumors is still increasing rapidly with increasing numbers of samples studied, as

demonstrated by saturation analysis (28). According to this report, creating a comprehensive

catalogue of somatic point mutations representing most cancer genes will require analyzing

~2 000 samples/tumor type. Therefore, prevalence studies using more sensitive and specific

methods and expanded sample sizes should be conducted.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Investigating signaling pathways associated with this novel oncogene provides

important information for combination therapies or resistance mechanisms against inhibitors.

The signaling pathway of fusion kinases can differ from WT kinases or fusion kinases with different partners, possibly due to different protein interactions. For instance, it was suggested

that cancer cells harboring the NPM-ALK fusion depend on STAT3 pathway activation, but

cancer cells harboring the EML4-ALK fusion do not (5). Similarly, the FGFR3-BAIAP2L1

fusion kinase induces phospho-STAT1, but the FGFR3-TACC3 fusion kinase cannot (18).

Therefore, we focused on FGFR3-BAIAP2L1 and investigated its associated signaling

pathways by comprehensive RNA-Seq analysis. We identified hyper-activation of the MAPK

pathway and suppression of several tumor suppressive pathways, such as the RB1, p53, or

CDKN2A pathways. In FGFR3-BAIAP2L1 cells, we observed that p53 or p21

downregulation correlated with a reversal of CDK4/Cyclin D suppression and RB

phosphorylation. These observations suggested that the FGFR3-BAIAP2L1 fusion suppresses

RB1 function and leads to E2F pathway activation, consistent with our IPA analysis. E2F

activation causes activation of the CDK2/Cyclin E complex, which can further induce p27

degradation (Fig. 3B). Inhibition of tumor suppressive pathways by oncogene fusions was

also reported with NPM-ALK (29). The theory of “oncogene-induced senescence” supports

the suppressive effect of the FGFR3-BAIAP2L1 fusion kinase (30). Oncogene-induced

senescence is a mechanism used by cells to stay in a premalignant stage, wherein cells do not

become malignant without an additional genetic alteration(s). This phenomenon has been

documented in cells harboring variants of BRAF (31), KRAS (32), and EGFR, (33) and involves p53 or RB pathway activation (34). Therefore, both MAPK pathway activation and

the escape from senescence through p53 or RB suppression may promote

FGFR3-BAIAP2L1-expressing cells to undergo transformation. This suggests that the

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

combined inhibition of suppressive activity and FGFR may result in synergistic antitumor

activity against cancers harboring FGFR3-BAIAP2L1.

The FGFR3-BAIAP2L1 fusion kinase is the first fusion kinase utilizing a BAR

domain as a dimerization motif. We demonstrated that the BAR domain is essential for

aberrant FGFR3 kinase activation and oncogenic activity (Fig. 4). Thus, small-molecule

FGFR inhibitors may facilitate targeted therapy for patients harboring the FGFR3-BAIAP2L1

rearrangement (Fig. 2F). An emerging clinical issue is the development of drug resistance,

and next-generation inhibitors against the same target are under clinical investigation because

these tumors may depend upon the same targets, even after resistance development. Similarly,

point mutations in the FGFR kinase domain are implicated in resistance against FGFR kinase

inhibitors (35, 36). Therefore, the development of alternative therapeutic antagonists of the same targets is important. Deletion of the BAR domain dramatically impairs dimerization activity (Fig. 5), suggesting that targeting the BAIP2L1 BAR domain may be a viable

therapeutic approach. Interestingly, BAIAP2L1 siRNA did not cause cytotoxicity in RT112/84

or HT1376 cells, which have WT BAIAP2L1 (Supplementary Fig. S3). Therefore, the

inhibition of BAIAP2L1 is expected to be safe, although further investigation is necessary.

In summary, we demonstrated that FGFR3-BAIAP2L1 exerts potent tumorigenic

activity through ligand-independent and constitutive dimerization via the BAR domain, and a

cell line harboring this gene fusion was sensitive to the FGFR inhibitor CH5183284/Debio

1347. We also detected this rearrangement in human clinical bladder and lung cancer specimens. Therefore, treating patients harboring FGFR gene fusions such as

FGFR3-BAIAP2L1 with CH5183284/Debio 1347 or other FGFR inhibitors may be a

promising approach in the future. CH5183284/Debio 1347 is currently under phase I clinical

investigation by Debiopharm International S.A. in patients harboring FGFR genetic alterations (NCT01948297).

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Disclosure of Potential Conflicts of Interest: All authors are employees of Chugai

Pharmaceutical Co., Ltd. The company was involved in the data analysis and the decision to publish this manuscript.

Acknowledgments

The authors thank Toshikazu Yamazaki and Yuko Aoki for helpful discussions. We thank Kiyoaki Sakata, Yasue Nagata, Yukari Nishitoh, Yuhsuke Ide, and Tsutomu Takahashi for performing pharmacological assays. We also thank Anne Vaslin, Hélène Maby-El Hajjami, and Corinne Moulon from Debiopharm International S.A. for their helpful discussions and technical support. This study was funded by the Chugai Pharmaceutical Co., Ltd.

Grant Support

This study was funded by the Chugai Pharmaceutical Co., Ltd.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked as advertisement in accordance with 18

U.S.C. Section 1734 solely to indicate this fact.

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

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Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Table 1. Prevalence of FGFR3-BAIAP2L1 rearrangements in clinical samples.

Tumor type N (%)

Adenocarcinoma 1 (3.6) (n = 28) Squamous cell Lung cancer 1 (3.6) (n = 28) Others 0 (0) (n = 27) Bladder cancer (n = 46) 2 (4.3) Head & neck cancer (n = 17) 0 (0) Gastroesophageal cancer (n=18) 0 (0)

Table 2. List of pathways activated or inhibited by FGFR3-BAIAP2L1, as suggested by analysis with IPA software.

Upstream Predicted state in Activation p-value regulator Rat-2_F3-B cells z-score of overlap RB1 Inhibited -2.95 9.5E-17 TP53 Inhibited -2.05 1.4E-12 RBL1 Inhibited -2.75 1.1E-11 CDKN2A Inhibited -2.31 4.9E-10 NUPR1 Inhibited -3.21 2.2E-06 E2F2 Activated 2.00 1.4E-13 E2F1 Activated 3.52 1.3E-12 TBX2 Activated 2.83 1.9E-08 CEBPB Activated 2.36 1.9E-05 STAT3 Activated 2.40 2.7E-04

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Figure legends

Figure 1. Detection of FGFR3-BAIAP2L1 rearrangements in clinical samples

(A) Amplified fragments were sequenced by Sanger sequencing. Representative sequence

waveforms are shown. The top image shows the waveform of the FGFR3-BAIAP2L1

junction site in a bladder cancer patient, and the bottom image shows that of WT FGFR3 in

the BFTC905 bladder cancer cell line. (B) Cell lines were analyzed with the break-apart

FISH assay. Fluorescein-labeled probes (green) hybridized to the 5 region of FGFR3 and

Texas red-labeled probes (red) hybridized to the 3 region. Separated signals indicate the

presence of the FGFR3-BAIAP2L1 fusion. (C) Break-apart FISH assay using a bladder cancer tissue microarray. Two positive cases are shown. Scale bars, 1 µm.

Figure 2. Confirmation of the oncogenic activity of FGFR3-BAIAP2L1

(A) Soft agar colony formation assay. Rat-2_mock, Rat-2_FGFR3, Rat-2_F3-B, and

Rat-2_BAIAP2L1 cells were cultured for 15 days in a 24-well plate. Cell morphologies were

recorded under a microscope. (B) Spheroid-formation activity. Cells were cultured for 14

days in a 96-well spheroid plate, and cell morphologies were recorded under a microscope.

The average diameter is shown (n = 6). (C) In vivo tumorigenic activity. Cells (5  106) were

implanted into nude mice. Tumor volumes of each group were measured at day 15 (n = 5).

(D) Cell growth inhibition by CH5183284/Debio 1347. SW780, Rat-2_FGFR3, 3T3_F3-B,

HT1376, and 3T3 EML4-ALK cells were seeded in 96-well spheroid plates and treated for 4 days with various concentrations of CH5183284/Debio 1347. Subsequently, cell viabilities were measured. (E) Inhibition of FRS or ERK phosphorylation. After a 2-hr treatment with

CH5183284/Debio 1347, SW780, Rat-2_FGFR3, 3T3_F3-B, HT1376, and 3T3 EML4-ALK cells were lysed and analyzed by western blot. (F) Antitumor activity of CH5183284/Debio

1347. Mice bearing SW780, Rat-2_F3-B, or HT1376 cells were treated with

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

CH5183284/Debio 1347 orally once daily for 11 days at the indicated doses. Tumor volumes

for each dose group were measured. Data shown are mean ± SD (n = 4–5). (G) Suppression

of FGFR or FRS phosphorylation. Mice bearing Rat-2_F3-B cells were orally administered

CH5183284/Debio 1347 at 100 mg/kg, and the tumors were collected and lysed at 4 h

post-dosing. Lysates were then analyzed by western blot

Figure 3. Analysis of FGFR3-BAIAP2L1 pathways

(A) Venn diagrams showing the number of commonly and differentially upregulated genes

(left) and downregulated genes (right) in Rat-2_F3-B, Rat-2_FGFR3, and Rat-2BAIAP2L1

cells. (B) Xenograft tumors derived from implantation of Rat-2_mock, Rat-2_FGFR3,

Rat-2_F3-B, and Rat-2_BAIAP2L1 cells into mice were lysed and analyzed by western blot

(n = 3).

Figure 4. Essentiality of the BAR domain in the FGFR3-BAIAP2L1 fusion kinase

(A) Schematic diagram of full-length FGFR3, FGFR3-BAIAP2L1 (F3-B), and the BAR deletion mutant of FGFR3-BAIAP2L1 (F3-B-ΔBAR). (B) Spheroid formation activity. Rat-2,

Rat-2_mock, Rat-2_FGFR3, Rat-2_F3-B, Rat-2_F3-B-ΔBAR, and Rat-2_BAIAP2L1 cells

were seeded into 96-well spheroid plates and cultured for 4 days. Subsequently, cell viabilities were measured (n = 3). (C) In vivo tumorigenic activity. Cells (5 106) were implanted subcutaneously into nude mice. Tumor volumes of each group were measured at day 14 (n = 5). (D) Ligand dependency. Cells were cultured in the presence of FGF1 (0, 0.1,

1, 10, and 100 ng/mL) and heparin (10 μg/mL) for 96 h, after which cell viabilities were measured (n = 3).

Oncogenic mechanisms and prevalence of FGFR3-BAIAP2L1

Figure 5. Dimerization activity of FGFR3-BAIAP2L1 lacking the BAR domain

(A) Schematic diagrams of full-length FGFR3 and FGFR3 variant constructs used in this

study. (B) Comparison of phospho-FGFR expression levels. 293 cells were transfected with

the expression vectors indicated in the diagram shown in (A). At 72 h post-transfection, cells

were lysed and analyzed by western blot. (C) Comparison of dimerization activities. 293 cells

were transfected with expression vectors encoding FGFR3, F3-B, or F3-B-ΔBAR and subsequently lysed. The lysates were immunoprecipitated with anti-FLAG M2 Affinity Gel and detected in western blots using an anti-FLAG or anti-Myc antibody. Total cell lysates

were also analyzed by western blot.

Fig. 1

A. FGFR3 exon18 BAIAP2L1 exon2 B. HCT116 RT112/84 (WT) (FGFR3-TACC3)

Bladder cancer patient #15

C G T C C A C C G A C A A T G T T A T G G A A C RT4 SW780 FGFR3 exon18 FGFR3 exon19 (FGFR3-TACC3) (FGFR3-BAIAP2L1)

Negative control BFTC905

C G T C C A C C G A C G A G T A C C T G G A C

C. Transitional cell Transitional cell bladder cancer bladder cancer (age: 57, grade: I (age: 43, grade: I-II stage: T1N0M0) stage: T1N0M0)

Fig. 2

A. Mock FGFR3 BAIAP2L1 F3-B D. 120

100

40 % of survival % of 20 B. Mock FGFR3 BAIAP2L1 F3-B 0 0.001 0.01 0.1 1 10 Concentration (µM) SW780 Rat2_F3-B 3T3_F3-B HT1376 3T3_EML4-ALK 163 ± 3.7 µm 167 ± 2.9 µm 154 ± 6.8 µm 548 ± 11 µm

ALK

C. E.

F3-B B B

Mock FGFR3 BAIAP2L1 2 - - - SW780 Rat _F3 3T3 _F3 HT1376 3T3 _EML4 CH5183284 1 µM - + - + - + - + - +

pFRS

FRS2

pERK

3 3 3 3 <100 mm <100 mm <100 mm >1000 mm ERK N=5 N=5 N=5 N=5 F. SW780 Rat-2_F3-B HT1376 (FGFR3-BAIAP2L1) (FGFR3-BAIAP2L1) (FGFR3 wild type) 1000 2400 1200

800 2000 1000 1600 800 600 1200 600 400 800 400 200 400 200 Tumor volume (mm3) volume Tumor (mm3) volume Tumor (mm3) volume Tumor 0 0 0 15 17 19 21 23 25 7 9 11 13 15 17 21 23 25 27 29 31 Days after the inoculation Days after the inoculation Days after the inoculation Vehicle 6.25 mg/kg Vehicle Vehicle 120 12.5100110708090 mg/kg 25 mg/kg 30 mg/kg 30 mg/kg 50 mg/kg151719212325 100 mg/kg 100 mg/kg 100 mg/kg

G. CH5183284 Vehicle 100mg/kg pFGFR

FGFR3

pFRS

FRS2 Downloaded from mct.aacrjournals.org on October 2, 2021. © 2015 American Association for Cancer Research. Author Manuscript Published OnlineFirst on January 14, 2015; DOI: 10.1158/1535-7163.MCT-14-0927-T Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Fig. 3

A. Up-regulated genes Down-regulated genes

FGFR3 FGFR3 215 273

193 540 328 135 284 119

1566 1916 220 2151 97 336

F3-B BAIAP2L1 F3-B BAIAP2L1

B. Mock FGFR3 F3-B BAIAP2L1 Mock FGFR3 F3-B BAIAP2L1

pFGFR pAKT AKT FGFR3 p53 BAIAP2L1 pERK p21 ERK pRB1

pMEK RB1

MEK p27

CyclinD1

Fig. 4

A. B. 30 FGFR3 TM

TK1 TK2 Coiled-coil 20 FGFR3-BAIAP2L1 (F3-B) TK1 TK2 BAR SH3 10

FGFR3-BAIAP2L1 ΔBAR (F3-B-ΔBAR) Ratio mock to TK1 TK2 SH3 0

BAIAP2L1 B BAR SH3 - F3 Mock ΔBAR Parent - FGFR3 B - BAIAP2L1

C. D. F3 2500 9

8 2000 7 6 1500 5 1000 4 3 500 Ratio mock to 2 1

Tumor volume volume Tumor (mm3) 0 0

- FGF1 B B - - F3 Mock ΔBAR F3 F3 - Mock FGFR3 ΔBAR B Parent - - FGFR3 BAIAP2L1 F3 BAIAP2L1

Fig. 5

A. B. FGFR3 TM TK1 TK2 Coiled-coil FGFR3-BAIAP2L1 (F3-B)

TK1 TK2 BAR SH3 ΔBAR ΔSH ΔBAR/ΔSH KD

- - - - B B B B B

FGFR3-BAIAP2L1 ΔBAR (F3-B-ΔBAR) - - - - -

TK1 TK2 SH3 Mock FGFR3 F3 F3 F3 F3 F3 FGFR3-BAIAP2L1 ΔSH (F3-B-ΔSH) TK1 TK2 BAR pY-FGFR FGFR3-BAIAP2L1 ΔBAR/ΔSH (F3-B- ΔBAR/ΔSH) TK1 TK2 FGFR3 FGFR3-BAIAP2L1 K508M (F3-B-KD) TK1 TK2 BAR SH3

K508M C. F3-B F3-B FGFR3 F3-B -ΔBAR FGFR3 F3-B -ΔBAR

Mock FLAG Myc FLAG+Myc FLAG Myc FLAG+Myc FLAG Myc FLAG+Myc Mock FLAG Myc FLAG+Myc FLAG Myc FLAG+Myc FLAG Myc FLAG+Myc

IB: Myc

IB: FLAG

IP: FLAG Input

Mechanism of oncogenic signal activation by the novel fusion kinase FGFR3-BAIAP2L1

Yoshito Nakanishi, Nukinori Akiyama, Toshiyuki Tsukaguchi, et al.

Mol Cancer Ther Published OnlineFirst January 14, 2015.

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