Claire Rooney

AZD4547: An Orally Bioavailable, Potent, and Selective Inhibitor of the Fibroblast Growth Factor Receptor Tyrosine Kinase Family

The fibroblast growth factor (FGF) signaling axis is increasingly implicated in tumorigenesis and chemoresistance. Several small-molecule FGF receptor (FGFR) kinase inhibitors are currently in clinical development; however, the predominant activity of the most advanced of these agents is against the kinase insert domain receptor (KDR), which compromises the FGFR selectivity. Here, we report the pharmacologic profile of AZD4547, a novel and selective inhibitor of the FGFR1, 2, and 3 tyrosine kinases. AZD4547 inhibited recombinant FGFR kinase activity in vitro and suppressed FGFR signaling and growth in tumor cell lines with deregulated FGFR expression. In a representative FGFR-driven human tumor xenograft model, oral administration of AZD4547 was well tolerated and resulted in potent dose-dependent antitumor activity, consistent with plasma exposure and pharmacodynamic modulation of tumor FGFR. Importantly, at efficacious doses, no evidence of anti-KDR-related effects were observed, confirming the in vivo FGFR selectivity of AZD4547. Taken together, our findings show that AZD4547 is a novel selective small-molecule inhibitor of FGFR with potent antitumor activity against FGFR-deregulated tumors in preclinical models. AZD4547 is under clinical investigation for the treatment of FGFR-dependent tumors.

High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial

UNLABELLED FGFR1 and FGFR2 are amplified in many tumor types, yet what determines response to FGFR inhibition in amplified cancers is unknown. In a translational clinical trial, we show that gastric cancers with high-level clonal FGFR2 amplification have a high response rate to the selective FGFR inhibitor AZD4547, whereas cancers with subclonal or low-level amplification did not respond. Using cell lines and patient-derived xenograft models, we show that high-level FGFR2 amplification initiates a distinct oncogene addiction phenotype, characterized by FGFR2-mediated transactivation of alternative receptor kinases, bringing PI3K/mTOR signaling under FGFR control. Signaling in low-level FGFR1-amplified cancers is more restricted to MAPK signaling, limiting sensitivity to FGFR inhibition. Finally, we show that circulating tumor DNA screening can identify high-level clonally amplified cancers. Our data provide a mechanistic understanding of the distinct pattern of oncogene addiction seen in highly amplified cancers and demonstrate the importance of clonality in predicting response to targeted therapy. SIGNIFICANCE Robust single-agent response to FGFR inhibition is seen only in high-level FGFR-amplified cancers, with copy-number level dictating response to FGFR inhibition in vitro, in vivo, and in the clinic. High-level amplification of FGFR2 is relatively rare in gastric and breast cancers, and we show that screening for amplification in circulating tumor DNA may present a viable strategy to screen patients. Cancer Discov; 6(8); 838-51. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 803.

Evaluating Robustness and Sensitivity of the NanoString Technologies nCounter Platform to Enable Multiplexed Gene Expression Analysis of Clinical Samples.

Analysis of clinical trial specimens such as formalin-fixed paraffin-embedded (FFPE) tissue for molecular mechanisms of disease progression or drug response is often challenging and limited to a few markers at a time. This has led to the increasing importance of highly multiplexed assays that enable profiling of many biomarkers within a single assay. Methods for gene expression analysis have undergone major advances in biomedical research, but obtaining a robust dataset from low-quality RNA samples, such as those isolated from FFPE tissue, remains a challenge. Here, we provide a detailed evaluation of the NanoString Technologies nCounter platform, which provides a direct digital readout of up to 800 mRNA targets simultaneously. We tested this system by examining a broad set of human clinical tissues for a range of technical variables, including sensitivity and limit of detection to varying RNA quantity and quality, reagent performance over time, variability between instruments, the impact of the number of fields of view sampled, and differences between probe sequence locations and overlapping genes across CodeSets. This study demonstrates that Nanostring offers several key advantages, including sensitivity, reproducibility, technical robustness, and utility for clinical application.

Targeting KRAS-dependent tumors with AZD4785, a high-affinity therapeutic antisense oligonucleotide inhibitor of KRAS

AZD4785 is a therapeutic antisense oligonucleotide targeting KRAS mRNA with promising preclinical antitumor activity and a favorable safety profile. An antisensible approach to targeting KRAS Mutations that cause activation of the KRAS oncogene are common in human cancer, including treatment-resistant tumor types such as lung and pancreatic cancer. KRAS has also proven to be notoriously difficult to target with small molecules. To overcome this issue, Ross et al. have turned to genetic technology, demonstrating an antisense oligonucleotide–based therapy for inhibiting KRAS. The antisense oligonucleotide used in this study was chemically modified, allowing systemic delivery through subcutaneous injection and avoiding the need for a specialized delivery vehicle. The authors tested the efficacy of this therapy in multiple mouse models of non–small cell lung cancer and evaluated its safety in primates, demonstrating its potential suitability for translation to humans. Activating mutations in KRAS underlie the pathogenesis of up to 20% of human tumors, and KRAS is one of the most frequently mutated genes in cancer. Developing therapeutics to block KRAS activity has proven difficult, and no direct inhibitor of KRAS function has entered clinical trials. We describe the preclinical evaluation of AZD4785, a high-affinity constrained ethyl–containing therapeutic antisense oligonucleotide (ASO) targeting KRAS mRNA. AZD4785 potently and selectively depleted cellular KRAS mRNA and protein, resulting in inhibition of downstream effector pathways and antiproliferative effects selectively in KRAS mutant cells. AZD4785-mediated depletion of KRAS was not associated with feedback activation of the mitogen-activated protein kinase (MAPK) pathway, which is seen with RAS-MAPK pathway inhibitors. Systemic delivery of AZD4785 to mice bearing KRAS mutant non–small cell lung cancer cell line xenografts or patient-derived xenografts resulted in inhibition of KRAS expression in tumors and antitumor activity. The safety of this approach was demonstrated in mice and monkeys with KRAS ASOs that produced robust target knockdown in a broad set of tissues without any adverse effects. Together, these data suggest that AZD4785 is an attractive therapeutic for the treatment of KRAS-driven human cancers and warrants further development.

A phase 1b open label multicentre study of AZD4547 in patients with advanced squamous cell lung cancers.

Purpose: Squamous cell lung cancers (SQCLC) account for 25% of all NSCLCs, yet the prognosis of these patients is poor and treatment options are limited. Amplified FGFR1 is one of the most common oncogenic events in SQCLCs, occurring in approximately 20% of cases. AZD4547 is a potent and selective FGFR1-3 inhibitor with antitumor activity in FGFR1-amplified SQCLC cell lines and patient-derived xenografts. Experimental Design: On the basis of these data, we performed a phase I study of AZD4547 in patients with previously treated stage IV FGFR1-amplified SQCLCs (NCT00979134). FGFR1 amplification (FGFR1:CEP8 ≥ 2) was determined by FISH. The primary endpoint was safety/tolerability. Secondary endpoints included antitumor activity, pharmacokinetics, pharmacodynamics, and molecular analyses. Results: Fifteen FGFR1-amplified patients were treated. The most common related adverse events (AE) were gastrointestinal and dermatologic. Grade ≥3–related AEs occurred in 3 patients (23%). Thirteen patients were evaluable for radiographic response assessment. The overall response rate was 8% (1 PR). Two of 15 patients (13.3%) were progression-free at 12 weeks, and the median overall survival was 4.9 months. Molecular tests, including next-generation sequencing, gene expression analysis, and FGFR1 immunohistochemistry, showed poor correlation between gene amplification and expression, potential genomic modifiers of efficacy, and heterogeneity in 8p11 amplicon. Conclusions: AZD4547 was tolerable at a dosage of 80 mg oral twice a day, with modest antitumor activity. Detailed molecular studies show that these tumors are heterogeneous, with a range of mutational covariates and stark differences in gene expression of the 8p11 amplicon that likely explain the modest efficacy of FGFR inhibition in this disease. Clin Cancer Res; 23(18); 5366–73. ©2017 AACR.

Structure-activity relationship of a series of non peptidic RGD integrin antagonists targeting α5β1: part 1.

Potent antagonists of the integrin α(5)β(1), which are RGD mimetics built from tyrosine are described. This paper describes the optimization of in vitro potency obtained by variation of two parts of the molecule, the central aromatic core and the amide moiety.

Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon.

FGFR1 amplification occurs in ~20% of sqNSCLC and trials with FGFR inhibitors have selected FGFR1 amplified patients by FISH. Lung cancer cell lines were profiled for sensitivity to AZD4547, a potent, selective inhibitor of FGFRs 1–3. Sensitivity to FGFR inhibition was associated with but not wholly predicted by increased FGFR1 gene copy number. Additional biomarker assays evaluating expression of FGFRs and correlation between amplification and expression in clinical tissues are therefore warranted. We validated nanoString for mRNA expression analysis of 194 genes, including FGFRs, from clinical tumour tissue. In a panel of sqNSCLC tumours 14.4% (13/90) were FGFR1 amplified by FISH. Although mean FGFR1 expression was significantly higher in amplified samples, there was significant overlap in the range of expression levels between the amplified and non-amplified cohorts with several non-amplified samples expressing FGFR1 to levels equivalent to amplified samples. Statistical analysis revealed increased expression of FGFR1 neighboring genes on the 8p12 amplicon (BAG4, LSM1 and WHSC1L1) in FGFR1 amplified tumours, suggesting a broad rather than focal amplicon and raises the potential for codependencies. High resolution aCGH analysis of pre-clinical and clinical samples supported the presence of a broad and heterogeneous amplicon around the FGFR1 locus. In conclusion, the range of FGFR1 expression levels in both FGFR1 amplified and non-amplified NSCLC tissues, together with the breadth and intra-patient heterogeneity of the 8p amplicon highlights the need for gene expression analysis of clinical samples to inform the understanding of determinants of response to FGFR inhibitors. In this respect the nanoString platform provides an attractive option for RNA analysis of FFPE clinical samples.

Identification of Pharmacodynamic Transcript Biomarkers in Response to FGFR Inhibition by AZD4547

The challenge of developing effective pharmacodynamic biomarkers for preclinical and clinical testing of FGFR signaling inhibition is significant. Assays that rely on the measurement of phospho-protein epitopes can be limited by the availability of effective antibody detection reagents. Transcript profiling enables accurate quantification of many biomarkers and provides a broader representation of pathway modulation. To identify dynamic transcript biomarkers of FGFR signaling inhibition by AZD4547, a potent inhibitor of FGF receptors 1, 2, and 3, a gene expression profiling study was performed in FGFR2-amplified, drug-sensitive tumor cell lines. Consistent with known signaling pathways activated by FGFR, we identified transcript biomarkers downstream of the RAS-MAPK and PI3K/AKT pathways. Using different tumor cell lines in vitro and xenografts in vivo, we confirmed that some of these transcript biomarkers (DUSP6, ETV5, YPEL2) were modulated downstream of oncogenic FGFR1, 2, 3, whereas others showed selective modulation only by FGFR2 signaling (EGR1). These transcripts showed consistent time-dependent modulation, corresponding to the plasma exposure of AZD4547 and inhibition of phosphorylation of the downstream signaling molecules FRS2 or ERK. Combination of FGFR and AKT inhibition in an FGFR2-mutated endometrial cancer xenograft model enhanced modulation of transcript biomarkers from the PI3K/AKT pathway and tumor growth inhibition. These biomarkers were detected on the clinically validated nanoString platform. Taken together, these data identified novel dynamic transcript biomarkers of FGFR inhibition that were validated in a number of in vivo models, and which are more robustly modulated by FGFR inhibition than some conventional downstream signaling protein biomarkers. Mol Cancer Ther; 15(11); 2802–13. ©2016 AACR.

Abstract 2407: Expression profiling of FGF-receptor pathway genes in squamous NSCLC tissue by Nanostring.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC FGFR1 amplifications have recently been identified in 22% of squamous non-small cell lung cancers (sqNSCLC) (Weiss et al., Sci Transl Med., 2(62), 2010) and in pre-clinical models this amplification confers sensitivity to FGFR inhibitor induced cell growth arrest and death (Zhang et al., Clin. Can. Res., In press). Ongoing clinical trials of FGFR inhibitors are selecting patients based on FGFR1 amplifications, as determined by FISH. The development of additional biomarker assays to evaluate the expression of FGFRs, FGF ligands and other potential modulators of response to support analysis of clinical tissues is warranted. We validated the Nanostring platform to allow gene expression (mRNA) analysis of 194 genes, including FGFRs and FGF ligands, from one 5μm section of formalin fixed paraffin embedded clinical tumor tissue. Intra- and inter-assay variability was low, as was variability between adjacent sections from the same tumor sample. Further validation of a subset of these genes by RT-PCR revealed a good correlation between platforms. A panel of 50 sqNSCLC tumors were analysed for FGFR1 gene amplification by FISH and for gene expression by Nanostring. FGFR1 amplfied tumours were enriched for high FGFR1 mRNA expression (p<0.02) compared to non-amplified samples, although a subset of non-amplified tumours also demonstrated increased FGFR1 mRNA expression. Immunohistochemical analysis, employing an FGFR1 specific antibody, revealed a correlation between FGFR1 mRNA levels and protein expression in these tumors. Nanostring analysis of additional genes on the 8p12 region, revealed that several of these, for example PPAPDC1B, ASH2L, TACC1 and in particular the FGFR1 neighbouring gene WHSC1L1 are highly expressed in FGFR1 amplified tumors (p<0.0001 for WHSC1L1). In contrast, expression of LETM2, located between WHSCL1 and FGFR1, was not significantly increased in amplified tumors. An FGF ligand expression profile was generated for each tumor, showing that a-FGF, b-FGF and FGF7 were the most abundantly expressed ligands in the sqNSCLC samples, with increased b-FGF expression detected in high FGFR1 expressing tumours. The expression of a panel of potential mediators of resistance to FGFR inhibitor therapy such as c-MET, EGFR and IGF1R were also profiled across the samples, revealing differential expression of these factors across each of the tumors and an inverse correlation between FGFR1 expression and ERBB3 expression. Taken together, these data validate the utility of the Nanostring platform for expression analysis of FGFR pathway genes using mRNA isolated from FFPE tumor samples and this platform can be used to assess the level of expression of potential modulators of clinical outcome. Citation Format: Claire Rooney, Dawn Baker, Neil R. Smith, Victoria Williams, Elizabeth A. Harrington, Carl Barrett, Paul D. Smith, Elaine Kilgour. Expression profiling of FGF-receptor pathway genes in squamous NSCLC tissue by Nanostring. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2407. doi:10.1158/1538-7445.AM2013-2407

Abstract 908: Identification of novel dynamic biomarkers of FGFR inhibition by the FGFR1,2 and 3 selective inhibitor AZD4547.

AZD4547 is an orally bio-available, highly selective and potent small molecule inhibitor, ATP competitive inhibitor of FGF receptors 1, 2 and 3. To identify novel dynamic transcript biomarkers of FGFR signalling inhibition by AZD4547, a gene expression profiling study was performed. Cell lines defined as sensitive or resistant to AZD4547 (n=10 for each class) were treated with AZD4547 or DMSO control for 2, 6 or 24 hours and processed for microarray analysis. Amongst those genes modulated by AZD4547, the MEK signature genes DUSP6 and ETV5, together with the MAPK pathway regulator SPRED1 were repressed on AZD4547 treatment across all sensitive cell lines over time, consistent with FGFR signalling through this pathway. Further in vivo validation using three FGFR sensitive/responsive xenograft models (SNU16, KMS11, KG1a) was performed. We observed time dependent repression (16h to 24h) of DUSP6, ETV5 and SPRED1 across all three xenograft models which was consistent with plasma exposure of AZD4547 in vivo. In addition, modulation of these transcript biomarkers corresponded with inhibition of phosphorylation of FGFR, FRS2 and ERK, supporting engagement of the FGFR signalling pathway. Taken together, these data identify novel dynamic biomarkers of FGFR inhibition in vivo. Citation Format: Oona Delpuech, Claire Rooney, Lorraine Mooney, Robert McEwen, Sarah Fenton, Dawn Baker, Robert Shaw, Jonathan Dry, Elaine Kilgour, Paul Smith. Identification of novel dynamic biomarkers of FGFR inhibition by the FGFR1,2 and 3 selective inhibitor AZD4547. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 908. doi:10.1158/1538-7445.AM2013-908