An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery

Penile squamous cell carcinoma (PSCC) is a rare malignancy in most parts of the world and the underlying mechanisms of this disease have not been fully investigated. About 30-50% of cases are associated with high-risk human papillomavirus (HPV) infection, which may have prognostic value. When PSCC becomes resistant to upfront therapies there are limited options, thus further research is needed in this venue. The extracellular domain-facing protein profile on the cell surface (i.e., the surfaceome) is a key area for biomarker and drug target discovery. This research employs computational methods combined with cell line translatomic (n = 5) and RNA-seq transcriptomic data from patient-derived tumors (n = 18) to characterize the PSCC surfaceome, evaluate the composition dependency on HPV infection, and explore the prognostic impact of identified surfaceome candidates. Immunohistochemistry (IHC) was used to validate the localization of select surfaceome markers. This analysis characterized a diverse surfaceome within patient tumors with 25% and 18% of the surfaceome represented by the functional classes of receptors and transporters, respectively. Significant differences in protein classes were noted by HPV status, with the most change being seen in transporter proteins (25%). IHC confirmed the robust surface expression of select surfaceome targets in the top 85% of expression and a superfamily immunoglobulin protein called BSG/CD147 was prognostic of survival. This study provides the first description of the PSCC surfaceome and its relation to HPV infection and sets a foundation for novel biomarker and drug target discovery in this rare cancer.

Abstract 6029: Multi-omic landscape of squamous cell lung cancer

Patients with squamous cell lung cancer (SCC) have high unmet medical need. Knowledge of these tumors is limited, and a lack of targetable genomic drivers means patients have few treatment options. To provide a detailed analysis on the influence of genomic alterations to proteome-level changes in SCC, we previously integrated DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 SCC patients. A major finding was identification of three proteomic subtypes, two of which made up the majority (87%) of tumors: the “Inflamed” subtype was enriched for B-cell rich tertiary lymphoid structures (TLS), and the “Redox” subtype was enriched for redox pathways and NFE2L2/KEAP1 alterations but had significantly less immune infiltration. We hypothesized these proteomic subtypes would give rise to distinct metabolic signatures. Therefore, we performed untargeted metabolomics on 87 tumors from the same cohort using chromatographic separation on a HILIC column, followed by analysis on a Q Exactive HF mass spectrometer. This analysis yielded 7,344 features corresponding to 7,072 unannotated metabolites and 272 identified metabolites. Glutathione, a key redox metabolite, was anticorrelated with immune score (R = -0.44, padj = 0.004) calculated from our transcriptomic data with the ESTIMATE algorithm, and glutathione was elevated in the Redox proteomic subtype (0.58 log2 ratio, padj = 9.87E-04). Consensus clustering was next used to identify novel metabolomic subtypes of SCC. Surprisingly, none of the five metabolomic subtypes we identified corresponded to proteomic subtype or NFE2L2/KEAP1 alteration (Fisher’s Exact test p-values > 0.05). The fifth subtype had 332 metabolites (26 identified) differentially expressed (> 1.5 fold-change, padj < 0.05) with ascorbate and aldarate metabolism as the top enriched pathway (padj = 3.36E-04). Interestingly, this fifth metabolomic subtype had significantly higher DNp63-alpha (p = 2.40E-05), a primary transcript of delta-N p63 that is known to promote non-small cell lung cancer. Ongoing integrative analyses across omic types will determine how p53, p63, and p73 transcripts influence these metabolomic subtypes, how these transcripts relate to the poor immune infiltration in some SCC tumors, and if these transcripts relate to novel metabolic vulnerabilities in SCC.

Citation Format: Paul Stewart, Ashley Lui, Eric Welsh, Dalia Ercan, Vanessa Rubio, Hayley Ackerman, Guohui Li, Bin Fang, Steven Eschrich, John Koomen, Elsa Flores, Eric Haura, Gina DeNicola. Multi-omic landscape of squamous cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6029.

An assessment of the penile squamous cell carcinoma surfaceome for therapeutic target discovery

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Background: There are limited options for relapsed penile squamous cell carcinoma (PSCC) patients after definitive therapy or chemo-refractory disease. Novel target discovery methods are needed to identify potential treatment options and the cell surface represents an actionable target for molecular and cell-based therapies. We evaluated the cell surface molecular catalogue (e.g., surfaceome) in PSCC to identify underexplored targets. Methods: To evaluate proteins enriched on the surface of PSCC cells, we screened published translatomics data from 5 PSCC cell lines (HPV-negative). Ribosome-bound RNA expression values were then analyzed using a validated surfaceome gene list (n=2,886 proteins) to infer surface presence, which were grouped by consensus protein classes. This was complemented by RNA-Seq (n=37) on resected PSCC tumors (HPV+=16, HPV- = 16, unknown HPV status = 5). We used immunohistochemistry (IHC) to assess protein expression and subcellular localization in PSCC tumors; stain intensity was assessed by a semi-quantitative H-score. Non-parametric statistics compared distributions and Kaplan-Meier analysis estimated overall survival (OS; defined from surgery to death or last follow-up) and groups were compared by log-rank testing. The open-source DRPPM-PATH-SURVEIOR app and R statistical software were used to perform analyses. Results: We identified 604 unique surfaceome proteins which were represented in the top 75% of expression in the PSCC cell line translatome. Half of these proteins have N-glycosylations and 49.5% classified as high-confidence surface targets. The largest proportions of surfaceome proteins included: Receptors (25.6%), Transporters (18.5%), and proteins with unclassified function (32.2%). Of note, 16.2% of this surfaceome linked to at least one compound in the DrugBank database.There was a moderate correlation between cell line and tumor surfaceome RNAs (top 75%; r =0.58, p < 2.2x10-16). We selected targets in the 99% (BSG; CD147; regulates MMPs and lactate transport), 90% (FGFR1; receptor tyrosine kinase) and 75% (SLC16A1; metabolite transporter) of the surfaceome expression. Tumor RNA levels for BSG, FGFR1 and SLC16A1 were elevated, but without differences based on HPV. IHC demonstrated robust expression in tumors with plasma membrane scoring being enriched compared to non-plasma membrane compartments (CD147, p =2.9x10-6; SLC16A1, p = 5.1x10-6; FGFR1, p = 0.007). Of note, patients with elevated BSG RNA (based on median log2 value) had worse OS (p = 0.018), though this lost significance after adjusting for HPV. No differences in OS were seen with FGFR1 or SLC16A1 expression. Conclusions: Our analysis of the surfaceome based on RNA expression was associated with increased protein levels in tumor tissues. Evaluation of the PSCC surfaceome may provide opportunity to investigate novel therapeutic targets, which may be actionable regardless of HPV status.

Oncogenic switch and single-agent MET inhibitor sensitivity in a subset of EGFR-mutant lung cancer

[Figure: see text].

Response Heterogeneity of EGFR and HER2 Exon 20 Insertions to Covalent EGFR and HER2 Inhibitors

Insertion mutations in EGFR and HER2 both occur at analogous positions in exon 20. Non-small cell lung cancer (NSCLC) patients with tumors harboring these mutations seldom achieve clinical responses to dacomitinib and afatinib, two covalent quinazoline-based inhibitors of EGFR or HER2, respectively. In this study, we investigated the effects of specific EGFR and HER2 exon 20 insertion mutations from NSCLC patients that had clinically achieved a partial response after dacomitinib treatment. We identified Gly770 as a common feature among the drug-sensitive mutations. Structural modeling suggested that this mutation may facilitate inhibitor binding to EGFR. Introduction of Gly770 into two dacomitinib-resistant EGFR exon 20 insertion mutants restored sensitivity to dacomitinib. Based on these findings, we used afatinib to treat an NSCLC patient whose tumor harbored the HER2 V777_G778insGSP mutation and achieved a durable partial response. We further identified secondary mutations in EGFR (T790M or C797S) and HER2 (C805S) that mediated acquired drug resistance in drug-sensitive EGFR or HER2 exon 20 insertion models. Overall, our findings identified a subset of EGFR and HER2 exon 20 insertion mutations that are sensitive to existing covalent quinazoline-based EGFR/HER2 inhibitors, with implications for current clinical treatment and next-generation small-molecule inhibitors. Cancer Res; 77(10); 2712-21. ©2017 AACR.

Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer

PURPOSE

Efforts to discover drugs that overcome resistance to targeted therapies in patients with rare oncogenic alterations, such as NTRK1 and ROS1 rearrangements, are complicated by the cost and protracted timeline of drug discovery.

EXPERIMENTAL DESIGN

In an effort to identify inhibitors of NTRK1 and ROS1, which are aberrantly activated in some patients with non-small cell lung cancer (NSCLC), we created and screened a library of existing targeted drugs against Ba/F3 cells transformed with these oncogenes.

RESULTS

This screen identified the FDA-approved drug cabozantinib as a potent inhibitor of CD74-ROS1-transformed Ba/F3, including the crizotinib-resistant mutants G2032R and L2026M (IC50 = 9, 26, and 11 nmol/L, respectively). Cabozantinib inhibited CD74-ROS1-transformed Ba/F3 cells more potently than brigatinib (wild-type/G2032R/L2026M IC50 = 30/170/200 nmol/L, respectively), entrectinib (IC50 = 6/2,200/3,500 nmol/L), and PF-06463922 (IC50 = 1/270/2 nmol/L). Cabozantinib inhibited ROS1 autophosphorylation and downstream ERK activation in transformed Ba/F3 cells and in patient-derived tumor cell lines. The IGF-1R inhibitor BMS-536924 potently inhibited CD74-NTRK1-transformed compared with parental Ba/F3 cells (IC50 = 19 nmol/L vs. > 470 nmol/L). A patient with metastatic ROS1-rearranged NSCLC with progression on crizotinib was treated with cabozantinib and experienced a partial response.

CONCLUSIONS

While acquired resistance to targeted therapies is challenging, this study highlights that existing agents may be repurposed to overcome drug resistance and identifies cabozantinib as a promising treatment of ROS1-rearranged NSCLC after progression on crizotinib. Clin Cancer Res; 23(1); 204-13. ©2016 AACR.

Abstract 890: TGFâ upregulation mediates growth retardation in EGFR T790M mutant non-small cell lung cancer

Introduction:

A subset of non-small cell lung cancer is driven by activating mutations in the epidermal growth factor receptor (EGFR). The majority of EGFR-driven lung cancers respond to EGFR kinase inhibitors gefitinib and erlotinib, although the clinical efficacy these inhibitors is limited by the development of drug resistance. A secondary missense mutation encoding EGFR T790M is the most prevalent resistance mechanism observed in patients, accounting for nearly 60% of relapse following gefitinib or erlotinib treatment. Although the T790M mutation enhances EGFR kinase activity, T790M harboring tumors exhibit indolent growth and are associated with favorable prognosis compared to tumors that acquire alternative mechanisms of drug resistance. The mechanism(s) underlying the indolent growth mediated by EGFR T790M are not well characterized.

Methods:

To identify the factor(s) mediating T790M associated growth retardation, we characterized T790M amplified drug resistant cells. EGFR mutant parental lung cancer cell lines PC9 and H3255 were selected through sequential treatment with gefitinib and the irreversible EGFR inhibitor dacomitinib. The resulting drug resistant cells, PC9DR and H3255DR, harbored amplified EGFR T790M and exhibited marked growth retardation. These T790M amplified models were characterized to identify factors conferring indolent growth. T790M expressing patient tumor samples were also analyzed to validate T790M associated changes.

Results:

Ectopic overexpression of EGFR T790M induced growth retardation in EGFR inhibitor-naïve cells. Incubation of parental PC9 cells in media conditioned on PC9DR cells was sufficient to slow PC9 growth rates, suggesting that a secreted factor was responsible for the growth retardation observed in the T790M amplified cells. A Luminex assay of PC9DR cells revealed upregulation of transforming growth factor beta 2 (TGFâ2), which was confirmed at the transcript level by qPCR. Treatment of parental PC9 cells with recombinant TGFâ was sufficient to induce slowed growth, while inhibition of TGFâ signaling using a TGFâ receptor inhibitor rescued growth rates in T790M amplified cell lines. Finally, T790M harboring patient tumor samples showed a trend of TGFâ2 transcript upregulation.

Conclusions:

We have demonstrated that TGFâ2 is upregulated in EGFR T790M amplified lung cancer cells, and is sufficient to elicit T790M associated growth retardation. The correlation between TGFâ expression and indolent growth of T790M expressing tumors identifies TGFâ as a potential biomarker to predict patient prognosis and outcome.

Citation Format: Claire E. Repellin, Pinar O. Eser, Marzia Capelletti, Takeshi Shimamura, Dalia Ercan, Chunxiao Xu, Nathanael S. Gray, Kwok-Kin Wong, Pasi A. Jänne. TGFâ upregulation mediates growth retardation in EGFR T790M mutant non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 890.

Overcoming EGFR(T790M) and EGFR(C797S) resistance with mutant-selective allosteric inhibitors

EGFR tyrosine kinase inhibitors (TKIs) gefitinib, erlotinib and afatinib are approved treatments for non-small cell lung cancers harboring activating mutations in the EGFR kinase^1,2, but resistance arises rapidly, most frequently due to the secondary T790M mutation within the ATP-site of the receptor.^3,4 Recently developed mutant-selective irreversible inhibitors are highly active against the T790M mutant^5,6, but their efficacy can be compromised by acquired mutation of C797, the cysteine residue with which they form a key covalent bond⁷. All current EGFR TKIs target the ATP-site of the kinase, highlighting the need for therapeutic agents with alternate mechanisms of action. Here we describe rational discovery of EAI045, an allosteric inhibitor that targets selected drug-resistant EGFR mutants but spares the wild type receptor. A crystal structure shows that the compound binds an allosteric site created by the displacement of the regulatory C-helix in an inactive conformation of the kinase. The compound inhibits L858R/T790M-mutant EGFR with low-nanomolar potency in biochemical assays, but as a single agent is not effective in blocking EGFR-driven proliferation in cells due to differential potency on the two subunits of the dimeric receptor, which interact in an asymmetric manner in the active state⁸. We observe dramatic synergy of EAI045 with cetuximab, an antibody therapeutic that blocks EGFR dimerization^9,10, rendering the kinase uniformly susceptible to the allosteric agent. EAI045 in combination with cetuximab is effective in mouse models of lung cancer driven by L858R/T790M EGFR and by L858R/T790M/C797S EGFR, a mutant that is resistant to all currently available EGFR TKIs. More generally, our findings illustrate the utility of purposefully targeting allosteric sites to obtain mutant-selective inhibitors.

Abstract 3644: Identification of existing targeted agents that inhibit NTRK and ROS1 in lung cancer

All patients with oncogenic driver mutations in non-small cell lung cancer (NSCLC) who are treated with a targeted agent will eventually develop resistance. In an effort to identify inhibitors of NTRK1 and ROS1, which are inappropriately activated in NSCLC, we created and screened a library of existing targeted drugs against BaF3 cells transformed with these oncogenes. This screen identified the FDA-approved drug cabozantinib as a potent inhibitor of CD74-ROS1 (IC50 = 9 nM), including the crizotinib-resistant mutants G2032R (IC50 = 26 nM) and L2026M (IC50 = 11 nM), with no inhibition of the parental BaF3 cells (IC50 &gt; 10 μM). AP26113, a dual ALK/EGFR inhibitor undergoing phase I/II clinical trials, also potently inhibited CD74-ROS1 (IC50 = 4 nM), including the crizotinib-resistant mutants G2032R (IC50 = 206 nM) and L2026M (IC50 = 84 nM), with weak inhibition of the parental BaF3 cells (IC50 &gt; 1 μM). Both cabozantinib and AP26113 inhibited ROS1 autophosphorylation and downstream ERK activation in CD74-ROS transformed BaF3 cells and in the ROS1-rearranged NSCLC cell line HCC78. The FGFR3 inhibitor dovitinib, which is in phase III clinical trials for renal cell carcinoma, potently inhibited NTRK1 compared to parental BaF3 cells (IC50 = 69 nM vs &gt; 1 μM), and blocked NTRK1 autophosphorylation and ERK activation. While acquired resistance to targeted therapies is a major clinical problem, this study highlights other existing agents that may overcome resistance, and identifies several promising candidates for clinical trials.

Citation Format: Curtis Chong, Dalia Ercan, Magda Bahcall, Marzia Capelletti, Nathanael Gray, Pasi Janne. Identification of existing targeted agents that inhibit NTRK and ROS1 in lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3644. doi:10.1158/1538-7445.AM2015-3644

Abstract LB-123: Analysis of cell-free plasma DNA (cfDNA) identifies 3 molecular subtypes of acquired resistance to AZD9291, a novel EGFR tyrosine kinase inhibitor (TKI), in patients (pts) with advanced lung cancer

Introduction: EGFR T790M is the most common mechanism of acquired resistance to EGFR TKIs in pts with EGFR-mutant lung cancer. AZD9291 is an irreversible, mutant-selective EGFR TKI developed to have potency against both sensiziting EGFR mutations and T790M. In the ongoing phase I study of AZD9291 (AURA, NCT01802632), the response rate in pts with T790M-positive lung cancer was &gt;60%. The molecular mechanism underlying acquired resistance to AZD9291 is not known.

Methods & Results: To explore for mechanisms of resistance to AZD9291, we studied cfDNA extracted from pretreatment and post-progression plasma collected on AURA.Next-generation sequencing (NGS) of cfDNA was first performed on an exploratory cohort of 7 pts. All exons of a 20 gene panel (including EGFR) underwent PCR amplification and NGS using an Illumina HiSeq. In 1 pt, NGS of progression plasma identified a new EGFR C797S mutation in exon 20, not present in pretreatment plasma. Stable expression of C797S in Ba/F3 cells induced a &gt;100-fold increase in IC50 to AZD9291 compared to EGFR activating and T790M mutations alone. To validate the plasma NGS, digital droplet PCR (ddPCR) assays were developed to detect key EGFR mutations including C797S. 15 T790M-positive cases were identified with progression plasma available for analysis. Serial plasma ddPCR showed that both the EGFR activating and T790M mutation levels decreased with AZD9291 treament and increased at progression, with 3 molecular subtypes of resistance apparent. In 6 pts (40%), C797S was detected in addition to T790M; NGS of resistance biopsies from 2 of these pts confirmed presence of acquired C797S. In 5 pts (33%), T790M was detected without evidence of C797S. Intriguingly, in 4 pts (27%), the T790M levels became undetectable with treatment despite high levels of the EGFR activating mutation at progression, suggesting overgrowth of a competing non-T790M resistance mechanism. Further NGS of progression plasma revealed additional evidence of the genomic heterogeneity of resistance. Individual sequencing reads indicate that C797S and T790M can occur either in cis or in trans (i.e. on competing resistant alleles). In the 2 pts with tumor NGS demonstrating C797S, plasma NGS identified both the DNA alteration seen in tumor as well as a second DNA alteration encoding for C797S.

Conclusion: Using complementary assays for genomic analyses of cfDNA, we identified 3 molecular subtypes of acquired resistance to AZD9291, including an EGFR C797S mutation never before reported in pts. Due to the key role of the C797 residue in drug binding, C797S is expected to induce resistance to all irreversible EGFR TKIs currently in clinical development. Plasma NGS revealed substantial genomic heterogeneity and highlights the need for combination therapies to effectively prevent or treat drug resistance in cancer.

Citation Format: Geoffrey R. Oxnard, Kenneth S. Thress, Cloud P. Paweletz, Enriqueta Felip, Byoung Chul Cho, Daniel Stetson, Brian Dougherty, Zhongwu Lai, Aleksandra Morkovets, Ana Vivancos, Yanan Kuang, Dalia Ercan, Mireille Cantarini, J Carl Barrett, Pasi A. Janne. Analysis of cell-free plasma DNA (cfDNA) identifies 3 molecular subtypes of acquired resistance to AZD9291, a novel EGFR tyrosine kinase inhibitor (TKI), in patients (pts) with advanced lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-123. doi:10.1158/1538-7445.AM2015-LB-123

Identification of Oncogenic and Drug-Sensitizing Mutations in the Extracellular Domain of FGFR2

The discovery of oncogenic driver mutations and the subsequent developments in targeted therapies have led to improved outcomes for subsets of lung cancer patients. The identification of additional oncogenic and drug-sensitive alterations may similarly lead to new therapeutic approaches for lung cancer. We identify and characterize novel FGFR2 extracellular domain insertion mutations and demonstrate that they are both oncogenic and sensitive to inhibition by FGFR kinase inhibitors. We demonstrate that the mechanism of FGFR2 activation and subsequent transformation is mediated by ligand-independent dimerization and activation of FGFR2 kinase activity. Both FGFR2-mutant forms are predominantly located in the endoplasmic reticulum and Golgi but nevertheless can activate downstream signaling pathways through their interactions with fibroblast growth factor receptor substrate 2 (FRS2). Our findings provide a rationale for therapeutically targeting this unique subset of FGFR2-mutant cancers as well as insight into their oncogenic mechanisms.

Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer

Irreversible pyrimidine-based EGFR inhibitors, including WZ4002, selectively inhibit both EGFR-activating and EGFR inhibitor-resistant T790M mutations more potently than wild-type EGFR. Although this class of mutant-selective EGFR inhibitors is effective clinically in lung cancer patients harboring EGFR(T790M), prior preclinical studies demonstrate that acquired resistance can occur through genomic alterations that activate ERK1/2 signaling. Here, we find that ERK1/2 reactivation occurs rapidly following WZ4002 treatment. Concomitant inhibition of ERK1/2 by the MEK inhibitor trametinib prevents ERK1/2 reactivation, enhances WZ4002-induced apoptosis, and inhibits the emergence of resistance in WZ4002-sensitive models known to acquire resistance via both T790M-dependent and T790M-independent mechanisms. Resistance to WZ4002 in combination with trametinib eventually emerges due to AKT/mTOR reactivation. These data suggest that initial cotargeting of EGFR and MEK could significantly impede the development of acquired resistance in EGFR-mutant lung cancer.

SIGNIFICANCE

Patients with EGFR-mutant lung cancer develop acquired resistance to EGFR and mutant-selective EGFR tyrosine kinase inhibitors. Here, we show that cotargeting EGFR and MEK can prevent the emergence of a broad variety of drug resistance mechanisms in vitro and in vivo and may be a superior therapeutic regimen for these patients.

Acquired EGFR C797S mutation mediates resistance to AZD9291 in non-small cell lung cancer harboring EGFR T790M

Here we studied cell-free plasma DNA (cfDNA) collected from subjects with advanced lung cancer whose tumors had developed resistance to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) AZD9291. We first performed next-generation sequencing of cfDNA from seven subjects and detected an acquired EGFR C797S mutation in one; expression of this mutant EGFR construct in a cell line rendered it resistant to AZD9291. We then performed droplet digital PCR on serial cfDNA specimens collected from 15 AZD9291-treated subjects. All were positive for the T790M mutation before treatment, but upon developing AZD9291 resistance three molecular subtypes emerged: six cases acquired the C797S mutation, five cases maintained the T790M mutation but did not acquire the C797S mutation and four cases lost the T790M mutation despite the presence of the underlying EGFR activating mutation. Our findings provide insight into the diversity of mechanisms through which tumors acquire resistance to AZD9291 and highlight the need for therapies that are able to overcome resistance mediated by the EGFR C797S mutation.

EGFR Mutations and Resistance to Irreversible Pyrimidine-Based EGFR Inhibitors

PURPOSE

Mutant selective irreversible pyrimidine-based EGFR kinase inhibitors, including WZ4002, CO-1686, and AZD9291, are effective in preclinical models and in lung cancer patients harboring the EGFR T790M gefitinib/erlotinib resistance mutation. However, little is known about how cancers develop acquired resistance to this class of EGFR inhibitors. We sought to identify and study EGFR mutations that confer resistance to this class of agents.

EXPERIMENTAL DESIGN

We performed an N-ethyl-N-nitrosourea (ENU) mutagenesis screen in EGFR-mutant (sensitizing alone or with concurrent EGFR T790M) Ba/F3 cells and selected drug-resistant clones. We evaluated the sensitivity of EGFR inhibitors in models harboring drug-resistant EGFR mutations.

RESULTS

We identified 3 major drug resistance mutations. EGFR L718Q, L844V, and C797S cause resistance to both WZ4002 and CO-1686 while, in contrast, only EGFR C797S leads to AZD9291 resistance. Cells containing an EGFR-sensitizing mutation, Del 19 or L858R, in conjunction with L718Q, L844V, or C797S retain sensitivity to quinazoline-based EGFR inhibitors, gefitinib and afatinib. The C797S mutation, in the presence of Del 19 or L858R and T790M, causes resistance to all current EGFR inhibitors, but L858R/T790M/C797S remains partially sensitive to cetuximab which leads to disruption of EGFR dimerization.

CONCLUSIONS

Our findings provide insights into resistance mechanisms to irreversible pyrimidine-based EGFR inhibitors and identify specific genomic contexts in which sensitivity is retained to existing clinical EGFR inhibitors. These findings will guide the development of new strategies to inhibit EGFR.

Tivantinib (ARQ 197) efficacy is independent of MET inhibition in non-small-cell lung cancer cell lines

MET targeted therapies are under clinical evaluation for non-small-cell lung cancer (NSCLC) patients. Tyrosine kinase inhibitors (TKI) against MET have varying degrees of specificity. Tivantinib (ARQ 197) is reported to be a non-ATP competitive selective MET inhibitor. We aimed to compare the activity of tivantinib to established MET TKIs in a panel of NSCLC cell lines characterized by their MET dependency and by different relevant genotypes. A549, H3122, PC9 and HCC827, their respective resistant clones PC9 GR4 and HCC827 GR6 and the MET amplified cell lines H1993 and EBC-1 were treated in vitro with tivantinib, crizotinib or PHA-665752. Crizotinib and PHA-665752 showed growth inhibition restricted to MET dependent cell lines. The pattern of activity was related to MET inhibition and downstream signaling inhibition of AKT and ERK1/2, resulting in G0/G1 cycle arrest and apoptosis. In contrast, tivantinib possessed more potent anti-proliferative activity that was not restricted to only MET dependent cell lines. Tivantinib did not inhibit cellular MET activity or phosphorylation of downstream signaling proteins AKT or ERK1/2 in either MET dependent or independent cell lines. Cell cycle analysis demonstrated that tivantinib induced a G2/M arrest and induced apoptosis. Tivantinib but not crizotinib effected microtubule dynamics, disrupting mitotic spindles by a mechanism consistent with it functioning as a microtubule depolymerizer. Tivantinib activity is independent of MET signaling in NSCLC and suggests alternative mechanisms of action that should be considered when interpreting the results from on-going clinical studies.

Pharmacological targeting of the pseudokinase Her3

Her3 (also known as ErbB3) belongs to the epidermal growth factor receptor tyrosine kinases and is well credentialed as an anti-cancer target but is thought to be 'undruggable' using ATP-competitive small molecules because it lacks appreciable kinase activity. Here we report what is to our knowledge the first selective Her3 ligand, TX1-85-1, that forms a covalent bond with Cys721 located in the ATP-binding site of Her3. We demonstrate that covalent modification of Her3 inhibits Her3 signaling but not proliferation in some Her3-dependent cancer cell lines. Subsequent derivatization with a hydrophobic adamantane moiety demonstrates that the resultant bivalent ligand (TX2-121-1) enhances inhibition of Her3-dependent signaling. Treatment of cells with TX2-121-1 results in partial degradation of Her3 and serendipitously interferes with productive heterodimerization between Her3 with either Her2 or c-Met. These results suggest that small molecules will be capable of perturbing the biological function of Her3 and ∼60 other pseudokinases found in human cells.

Identification of recurrent FGFR3-TACC3 fusion oncogenes from lung adenocarcinoma

PURPOSE

Targetable oncogenic alterations are detected more commonly in patients with non-small cell lung cancer (NSCLC) who never smoked cigarettes. For such patients, specific kinase inhibitors have emerged as effective clinical treatments. However, the currently known oncogenic alterations do not account for all never smokers who develop NSCLC. We sought to identify additional oncogenic alterations from patients with NSCLC to define additional treatment options.

EXPERIMENTAL DESIGN

We analyzed 576 lung adenocarcinomas from patients of Asian and Caucasian ethnicity. We identified a subset of cancers that did not harbor any known oncogenic alteration. We performed targeted next-generation sequencing (NGS) assay on 24 patients from this set with >75% tumor cell content.

RESULTS

EGFR mutations were the most common oncogenic alteration from both Asian (53%) and Caucasian (41.6%) patients. No known oncogenic alterations were present in 25.7% of Asian and 31% of Caucasian tumor specimens. We identified a FGFR3-TACC3 fusion event in one of 24 patients from this subset using targeted NGS. Two additional patients harboring FGFR3-TACC3 were identified by screening our entire cohort (overall prevalence, 0.5%). Expression of FGFR3-TACC3 led to IL3 independent growth in Ba/F3 cells. These cells were sensitive to pan-fibroblast growth factor receptor (pan-FGFR) inhibitors but not the epidermal growth factor (EGFR) inhibitor gefitinib.

CONCLUSIONS

FGFR3-TACC3 rearrangements occur in a subset of patients with lung adenocarcinoma. Such patients should be considered for clinical trials featuring FGFR inhibitors.

Abstract 1832: Combined EGFR and MEK inhibition prevents the emergence of drug resistance in EGFR mutant non-small cell lung cancer (NSCLC)

Background: EGFR inhibitors are effective clinical therapies for EGFR mutant NSCLC, but efficacy is limited by the development of acquired drug resistance. The mechanisms of resistance include secondary mutations in EGFR (T790M) and activation of compensatory signaling pathways (MET, IGFR and AXL). Mutant selective EGFR inhibitors (WZ4002, CO-1686 and AZD9291) are effective in preclinical and clinical models of EGFR T790M. Our lab has demonstrated that reactivation of ERK signaling is a mechanism of resistance to WZ4002 (WZ) which could be reversed or prevented by using a combination of WZ and MEK inhibitors. Given the broad array of possible EGFR inhibitor resistance mechanisms, we evaluated whether WZ combined with the MEK inhibitor trametinib (TRA) can prevent the emergence of resistance in vitro and in vivo.

Methods and Results: We developed a plate based resistance assay in which 350 cells/well are plated in 96 well plates and treated weekly. This system allows for evaluation of drug efficacy over weeks of treatment and can be used to measure both time to development and frequency of drug resistance. Given that ERK reactivation can cause resistance to WZ, we evaluated WZ, TRA or the combination thereof (WZ/TRA) using PC9 cells. Single agents led to 100% resistance in 2-3 weeks, versus 5% with WZ/TRA in 24 weeks. We then tested WZ/TRA in 5 additional EGFR TKI sensitive cell lines, including several known to develop acquired resistance to gefitinib (HCC827, MET amplification; HCC4006, EMT or FGFR activation; HCC2279; FGFR activation; H3255, T790M; HCC2935). In all cases, WZ/TRA significantly reduced the emergence of drug resistant clones compared to each single agent. In models with established drug resistance mechanisms, WZ/TRA was effective in 3/3 models with T790M mutations, but not (0/5) in models with established non-T790M resistance mechanisms. In models where WZ/TRA was effective, the combination led to increased apoptosis compared to single agents and effective inhibition of ERK signaling. We also evaluated the effectiveness of the WZ/TRA combination in vivo using EGFR L858R/T790M genetically engineered mouse model and PC9GR4 (T790M+) xenografts. Combination WZ/TRA treatment prevented tumor outgrowth for 24 weeks in 5 EGFR L858R/T790M GEMM mice whereas individual treatments did not. Additionally, we found that WZ/TRA combination treatment, but not single agents, could cure 7/15 xenograft tumors as assessed by lack of tumor regrowth after treatment cessation.

Conclusion: Our studies suggest that the combination of a mutant selective EGFR inhibitor and a MEK inhibitor can prevent the emergence of both T790M and non-T790M mediated drug resistance mechanisms. This strategy is more effective at preventing (6/6) than treating (3/8) cancers with established drug resistance mechanisms and should be evaluated in clinical trials in EGFR TKI naïve EGFR mutant NSCLC patients.

Citation Format: Erin M. Tricker, Chunxiao Xu, Dalia Ercan, Atsuko Ogino, Kwok-kin Wong, Pasi Janne. Combined EGFR and MEK inhibition prevents the emergence of drug resistance in EGFR mutant non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1832. doi:10.1158/1538-7445.AM2014-1832

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer

We identified new gene fusions in patients with lung cancer harboring the kinase domain of the NTRK1 gene that encodes the high-affinity nerve growth factor receptor (TRKA protein). Both the MPRIP-NTRK1 and CD74-NTRK1 fusions lead to constitutive TRKA kinase activity and are oncogenic. Treatment of cells expressing NTRK1 fusions with inhibitors of TRKA kinase activity inhibited autophosphorylation of TRKA and cell growth. Tumor samples from 3 of 91 patients with lung cancer (3.3%) without known oncogenic alterations assayed by next-generation sequencing or fluorescence in situ hybridization demonstrated evidence of NTRK1 gene fusions.

Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR

mTOR is a highly conserved serine/threonine protein kinase that serves as a central regulator of cell growth, survival, and autophagy. Deregulation of the PI3K/Akt/mTOR signaling pathway occurs commonly in cancer and numerous inhibitors targeting the ATP-binding site of these kinases are currently undergoing clinical evaluation. Here, we report the characterization of Torin2, a second-generation ATP-competitive inhibitor that is potent and selective for mTOR with a superior pharmacokinetic profile to previous inhibitors. Torin2 inhibited mTORC1-dependent T389 phosphorylation on S6K (RPS6KB1) with an EC(50) of 250 pmol/L with approximately 800-fold selectivity for cellular mTOR versus phosphoinositide 3-kinase (PI3K). Torin2 also exhibited potent biochemical and cellular activity against phosphatidylinositol-3 kinase-like kinase (PIKK) family kinases including ATM (EC(50), 28 nmol/L), ATR (EC(50), 35 nmol/L), and DNA-PK (EC(50), 118 nmol/L; PRKDC), the inhibition of which sensitized cells to Irradiation. Similar to the earlier generation compound Torin1 and in contrast to other reported mTOR inhibitors, Torin2 inhibited mTOR kinase and mTORC1 signaling activities in a sustained manner suggestive of a slow dissociation from the kinase. Cancer cell treatment with Torin2 for 24 hours resulted in a prolonged block in negative feedback and consequent T308 phosphorylation on Akt. These effects were associated with strong growth inhibition in vitro. Single-agent treatment with Torin2 in vivo did not yield significant efficacy against KRAS-driven lung tumors, but the combination of Torin2 with mitogen-activated protein/extracellular signal-regulated kinase (MEK) inhibitor AZD6244 yielded a significant growth inhibition. Taken together, our findings establish Torin2 as a strong candidate for clinical evaluation in a broad number of oncologic settings where mTOR signaling has a pathogenic role.

Resistance to irreversible EGF receptor tyrosine kinase inhibitors through a multistep mechanism involving the IGF1R pathway

The clinical efficacy of EGF receptor (EGFR) kinase inhibitors gefitinib and erlotinib is limited by the development of drug resistance. The most common mechanism of drug resistance is the secondary EGFR T790M mutation. Strategies to overcome EGFR T790M-mediated drug resistance include the use of mutant selective EGFR inhibitors, including WZ4002, or the use of high concentrations of irreversible quinazoline EGFR inhibitors such as PF299804. In the current study, we develop drug-resistant versions of the EGFR-mutant PC9 cell line, which reproducibly develops EGFR T790M as a mechanism of drug resistance to gefitinib. Neither PF299804-resistant nor WZ4002-resistant clones of PC9 harbor EGFR T790M. Instead, they have shown activated insulin-like growth factor receptor (IGF1R) signaling as a result of loss of expression of IGFBP3 with the IGF1R inhibitor, BMS 536924, restoring EGFR inhibitor sensitivity. Intriguingly, prolonged exposure to either PF299804 or WZ4002 results in the emergence of a more drug-resistant subclone that exhibits ERK activation. A MEK inhibitor, CI-1040, partially restores sensitivity to the EGFR/IGF1R inhibitor combination. Moreover, an IGF1R or MEK inhibitor used in combination with either PF299804 or WZ4002 completely prevents the emergence of drug-resistant clones in this model system. Our studies suggest that more effective means of inhibiting EGFR T790M will prevent the emergence of this common drug resistance mechanism in EGFR-mutant non-small cell lung cancer. However, multiple drug resistance mechanisms can still emerge. Preventing the emergence of drug resistance, by targeting pathways that become activated in resistant cancers, may be a more effective clinical strategy.

Reactivation of ERK signaling causes resistance to EGFR kinase inhibitors

The clinical efficacy of epidermal growth factor receptor (EGFR) kinase inhibitors is limited by the development of drug resistance. The irreversible EGFR kinase inhibitor WZ4002 is effective against the most common mechanism of drug resistance mediated by the EGFR T790M mutation. Here, we show, in multiple complementary models, that resistance to WZ4002 develops through aberrant activation of extracellular signal-regulated kinase (ERK) signaling caused by either an amplification of mitogen-activated protein kinase 1 (MAPK1) or by downregulation of negative regulators of ERK signaling. Inhibition of MAP-ERK kinase (MEK) or ERK restores sensitivity to WZ4002 and prevents the emergence of drug resistance. We further identify MAPK1 amplification in an erlotinib-resistant EGFR-mutant non-small cell lung carcinoma patient. In addition, the WZ4002-resistant MAPK1-amplified cells also show an increase both in EGFR internalization and a decrease in sensitivity to cytotoxic chemotherapy. Our findings provide insights into mechanisms of drug resistance to EGFR kinase inhibitors and highlight rational combination therapies that should be evaluated in clinical trials.

Discovery of recurrent KIF5B-RET fusions and other targetable alterations from clinical NSCLC specimens

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Background: Many NSCLCs have driving oncogenic alterations including in EGFR, KRAS, ERBB2, BRAF, ALK and ROS1. Clinically effective drugs are approved for EGFR and ALK and clinical trials are underway for other genomic targets. Thus having a means of identifying genomic alterations in routine formalin fixed paraffin embedded (FFPE) clinical specimens is critical. Methods: We sequenced 24 FFPE NSCLC specimens with a next generation sequencing (NGS) assay that captures and sequences 2574 coding exons of 145 cancer relevant genes plus 37 introns from 14 genes often rearranged in cancer. Tumors from 643 additional patients were genotyped for KIF5B-RET. Results: We identified 50 alterations in 21 genes with at least one in 83% (20/24) of tumors (range 1-7). In 72% (36/50) of NSCLCs, at least one alteration was associated with a current clinical treatment or targeted therapy trial, including mutations in KRAS, BRAF, EGFR, MDM2, CDKN2A, CCNE1, CDK4, NF1 and PIK3CA. We also found an 11,294,741 bp pericentric inversion on chromosome 10 generating a novel gene fusion joining exons 1-15 of KIF5B to exons 12-20 of RET (K15:R12) in a Caucasian never smoker. This fusion gene contains the kinesin motor and coiled-coil domains of KIF5B and the entire RET tyrosine kinase domain. In 643 additional tumors we identified 11 fusion positive patients who were all wild type for known oncogenes (frequency of 6.3% (10/159)). Four unique KIF5B-RET variants were found: 8 K15:R12, 3 K16:R12, 1 K22:R12 and 1 K15:R11. We introduced K15:R12 into Ba/F3 cells and observed IL-3 independent growth consistent with oncogenic transformation. KIF5B-RET Ba/F3 cells were sensitive to sunitinib, sorafenib and vandetinib, multi-targeted kinase inhibitors that inhibit RET, but not gefitinib, an EGFR kinase inhibitor. Sunitinib, but not gefitinib, inhibited RET phosphorylation in these cells. Conclusions: We identified both known and novel genomic alterations from NSCLC FFPE specimens using a single test. Our findings suggest that RET inhibitors should be tested in prospective clinical trials in NSCLC patients bearing KIF5B-RET rearrangements and that NGS is a feasible approach to stratifying patients for treatment based on their genomic profiles.

Combined EGFR/MET or EGFR/HSP90 inhibition is effective in the treatment of lung cancers codriven by mutant EGFR containing T790M and MET

Tyrosine kinase inhibitors (TKI) that target the EGF receptor (EGFR) are effective in most non-small cell lung carcinoma (NSCLC) patients whose tumors harbor activating EGFR kinase domain mutations. Unfortunately, acquired resistance eventually emerges in these chronically treated cancers. Two of the most common mechanisms of acquired resistance to TKIs seen clinically are the acquisition of a secondary "gatekeeper" T790M EGFR mutation that increases the affinity of mutant EGFR for ATP and activation of MET to offset the loss of EGFR signaling. Although up to one-third of patient tumors resistant to reversible EGFR TKIs harbor concurrent T790M mutation and MET amplification, potential therapies for these tumors have not been modeled in vivo. In this study, we developed a preclinical platform to evaluate potential therapies by generating transgenic mouse lung cancer models expressing EGFR-mutant Del19-T790M or L858R-T790M, each with concurrent MET overexpression. We found that monotherapy targeting EGFR or MET alone did not produce significant tumor regression. In contrast, combination therapies targeting EGFR and MET simultaneously were highly efficacious against EGFR TKI-resistant tumors codriven by Del19-T790M or L858R-T790M and MET. Our findings therefore provide an in vivo model of intrinsic resistance to reversible TKIs and offer preclinical proof-of-principle that combination targeting of EGFR and MET may benefit patients with NSCLC.

Abstract 4832: Novel EGFR mutations that cause drug resistance to irreversible pyrimidine but not quinazoline based EGFR inhibitors

Background: Oncogenic EGFR T790M causes drug resistance to quinazoline based EGFR kinase inhibitors by increasing ATP affinity (Yun PNAS 2008). Mutant selective irreversible pyrimidine EGFR kinase inhibitor, WZ4002, is effective in non-small cell lung cancer (NSCLC) models harboring EGFR T790M (Zhou Nature 2009). We aimed to determine potential mechanisms of resistance to WZ4002 and explore alternative strategies to overcome acquired resistance to pyrimidine based EGFR inhibitors. Methods and Results: We performed an ENU mutagenesis screen in Ba/F3 cells expressing EGFR L858R, L858R/T790M, Del E746_A750 and Del E746_A750/T790M followed by culture in the presence of WZ4002 (100 nM or 1 μM). Using RT-PCR, we sequenced resistant clones for secondary EGFR mutations. No EGFR T790M mutations were identified. We detected novel secondary EGFR L718Q (9/27; 33%) or L844V (1/27; 3%) mutations in the drug resistant cells. We also recovered the EGFR C797S (1/27; 3%) mutation previously known to prevent covalent binding and decrease potency of WZ4002. Unlike EGFR T790M, EGFR L718Q and EGFR L844V did not lead to constitutive EGFR phosphorylation, were not transforming in Ba/F3 cells and required EGF for proliferation and survival. The EGFR L858R/L844V Ba/F3 cells were resistant to WZ4002 (IC50 0.7 μM) but sensitive to irreversible quinazoline EGFR inhibitors CL-387,785, HKI-272 (neratinib) and BIBW2992 (afatinib) (IC50 values all &lt; 10 nM). Similar findings were observed with the EGFR L858R/L718Q cells although the IC50 values were slightly higher (100 nM or less) and with the Del E746_A750/L718Q and Del E746_A750/L844V cells. All triple mutants harboring EGFR T790M (e.g. L858R/T790M/L844V) were resistant to WZ4002 and irreversible quinazoline EGFR inhibitors. EGFR L858R/L844V and L858R/L718Q Ba/F3 cells were growth inhibited by clinical concentrations (1 μM) of gefitinib and the combination of 1 μM gefitinib and 100 nM WZ4002 completely prevented the emergence of resistant clones in our ENU assay. Using structural modeling, both the L718Q and L844V mutations likely lead to steric hindrance and could impact WZ4002 binding. To verify this hypothesis, we developed a biotinylated-WZ4002 compound and used it to assay binding to different EGFR mutant proteins. This agent effectively bound to EGFR L858R and DelE746_A750 (with or without T790M). However, in the presence of a concurrent L718Q or L844V mutation, protein binding was significantly reduced, consistent with the reduced in vitro efficacy in the Ba/F3 cells. Conclusions: We identify novel EGFR mutations that confer drug resistance to irreversible pyrimidine but not quinazoline EGFR kinase inhibitors. Our findings have implications for understanding drug resistance mechanisms and for the development of combinations of EGFR kinase inhibitors as therapies for cancer patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4832. doi:1538-7445.AM2012-4832

Abstract LB-88: Identification of recurrent oncogenic KIF5B-RET rearrangements in non-small cell lung cancer

Background: A large number of non-small cell lung cancer (NSCLC) cases from never/former light smokers can be explained by driving oncogenic alterations in EGFR, KRAS, ERBB2, BRAF, ALK and ROS1. EGFR and ALK targeted tyrosine kinase inhibitors are effective clinical therapies for EGFR mutant and ALK rearranged NSCLC, respectively. We wished to study cancers that do not harbor a known genomic alteration in order to identify novel therapeutic targets that may increase treatment options for NSCLC patients. Methods and Results: We initially sequenced a NSCLC specimen from a 44 year old Caucasian never smoker in a CLIA certified lab (Foundation Medicine) using a next generation sequencing assay that captures and sequences 2574 coding exons representing 145 cancer relevant genes plus 37 introns from 14 genes frequently rearranged in cancer. We identified an 11,294,741 bp pericentric inversion on chromosome 10 generating a novel gene fusion joining exons 1-15 of KIF5B to exons 12-20 of RET (K15:R12). This fusion gene contains the kinesin motor and coiled-coil domains of KIF5B and the entire tyrosine kinase domain of RET. Expression of RET was confirmed by immunohistochemistry (IHC) and cDNA sequencing detected a 7.3-fold RET expression increase beginning at exon 12 relative to exons 1-11. Screening of additional 117 NSCLC patients using RET IHC identified 22 positive cases; sequencing of 15/22 of these identified 1 additional patient with a KIF5B-RET fusion. We also evaluated 526 tumors from never/former limited smokers (121 Caucasian and 405 Asian) and identified 10 additional (1/121 Caucasian (0.8%) and 9/405 Asian (2%)) positive patients. All fusion positive tumors were wild type for known oncogenes (frequency of 6.3 % (10/159) in WT patients). Four unique KIF5B-RET variants were identified: 8 K15:R12 (variant 1), 3 K16:R12 (variant 2), 1 K22:R12 (variant 3) and 1 K15:R11 (variant 4). We introduced K15:R12 (variant 1) into Ba/F3 cells and observed IL-3 independent growth consistent with oncogenic transformation. These KIF5B-RET Ba/F3 cells were sensitive to sunitinib, sorafenib and vandetinib, multi-targeted kinase inhibitors that inhibit RET, but not gefitinib, an EGFR kinase inhibitor. Sunitinib, but not gefitinib, inhibited RET phosphorylation in the KIF5B-RET Ba/F3 cells. Conclusions: We identify a novel oncogenic KIF5B-RET fusion gene in a subset of NSCLC patients lacking other known driver mutations. Our findings suggest that RET kinase inhibitors should be tested in prospective clinical trials for therapeutic benefit in NSCLC patients bearing KIF5B-RET rearrangements.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-88. doi:1538-7445.AM2012-LB-88

Activation of ERBB2 signaling causes resistance to the EGFR-directed therapeutic antibody cetuximab

Cetuximab, an antibody directed against the epidermal growth factor receptor, is an effective clinical therapy for patients with colorectal, head and neck, and non-small cell lung cancer, particularly for those with KRAS and BRAF wild-type cancers. Treatment in all patients is limited eventually by the development of acquired resistance, but little is known about the underlying mechanism. Here, we show that activation of ERBB2 signaling in cell lines, either through ERBB2 amplification or through heregulin up-regulation, leads to persistent extracellular signal-regulated kinase 1/2 signaling and consequently to cetuximab resistance. Inhibition of ERBB2 or disruption of ERBB2/ERBB3 heterodimerization restores cetuximab sensitivity in vitro and in vivo. A subset of colorectal cancer patients who exhibit either de novo or acquired resistance to cetuximab-based therapy has ERBB2 amplification or high levels of circulating heregulin. Collectively, these findings identify two distinct resistance mechanisms, both of which promote aberrant ERBB2 signaling, that mediate cetuximab resistance. Moreover, these results suggest that ERBB2 inhibitors, in combination with cetuximab, represent a rational therapeutic strategy that should be assessed in patients with cetuximab-resistant cancers.

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies

Applying a next-generation sequencing assay targeting 145 cancer-relevant genes in 40 colorectal cancer and 24 non-small cell lung cancer formalin-fixed paraffin-embedded tissue specimens identified at least one clinically relevant genomic alteration in 59% of the samples and revealed two gene fusions, C2orf44-ALK in a colorectal cancer sample and KIF5B-RET in a lung adenocarcinoma. Further screening of 561 lung adenocarcinomas identified 11 additional tumors with KIF5B-RET gene fusions (2.0%; 95% CI 0.8-3.1%). Cells expressing oncogenic KIF5B-RET are sensitive to multi-kinase inhibitors that inhibit RET.

A novel ALK secondary mutation and EGFR signaling cause resistance to ALK kinase inhibitors

Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKI), including crizotinib, are effective treatments in preclinical models and in cancer patients with ALK-translocated cancers. However, their efficacy will ultimately be limited by the development of acquired drug resistance. Here we report two mechanisms of ALK TKI resistance identified from a crizotinib-treated non-small cell lung cancer (NSCLC) patient and in a cell line generated from the resistant tumor (DFCI076) as well as from studying a resistant version of the ALK TKI (TAE684)-sensitive H3122 cell line. The crizotinib-resistant DFCI076 cell line harbored a unique L1152R ALK secondary mutation and was also resistant to the structurally unrelated ALK TKI TAE684. Although the DFCI076 cell line was still partially dependent on ALK for survival, it also contained concurrent coactivation of epidermal growth factor receptor (EGFR) signaling. In contrast, the TAE684-resistant (TR3) H3122 cell line did not contain an ALK secondary mutation but instead harbored coactivation of EGFR signaling. Dual inhibition of both ALK and EGFR was the most effective therapeutic strategy for the DFCI076 and H3122 TR3 cell lines. We further identified a subset (3/50; 6%) of treatment naive NSCLC patients with ALK rearrangements that also had concurrent EGFR activating mutations. Our studies identify resistance mechanisms to ALK TKIs mediated by both ALK and by a bypass signaling pathway mediated by EGFR. These mechanisms can occur independently, or in the same cancer, suggesting that the combination of both ALK and EGFR inhibitors may represent an effective therapy for these subsets of NSCLC patients.

Abstract 4736: Amplification of ERK2 mediates resistance to the novel irreversible EGFR inhibitor WZ4002

Background: EGFR T790M causes clinical resistance to the quinazoline EGFR kinase inhibitors gefitinib and erlotinib in non-small cell lung cancer. Amplification of EGFR T790M causes resistance to the irreversible quinazoline EGFR inhibitor PF00299804 (Ercan etl al. Oncogene 2010). A novel T790M selective irreversible pyrimidine EGFR kinase inhibitor, WZ4002, is effective in NSCLC models harboring EGFR T790M (Zhou, W, Ercan, D et al., Nature 2009). The mechanism(s) of resistance to this class of irreversible EGFR inhibitors have not been explored.

Methods and Results: We exposed the Gefitinib resistant PC9 GR cells (EGFR del E746_A750/T790M; IC50 to WZ4002: ∼30nM) to increasing concentrations of WZ4002 to generate PC9 GW resistant cells (IC50 to WZ4002 ∼10µM) and isolated several resistant clones. The PC9 GWR cells contain EGFR del E746_A750/T790M but do not harbor additional EGFR mutations and are cross resistant to the irreversible quinazoline EGFR inhibitor BIBW2992. The PC9 GWR cells demonstrate an increase in basal phosphorylation of ERK2 but not ERK1 as well as total protein compared to parental PC9 GR cells. WZ4002 effectively inhibits EGFR phosphorylation but not ERK 2 phosphorylation in the PC9 GWR cells whereas in the PC9 GR cells WZ4002 inhibits both EGFR and ERK 1/2 phosphorylation. Furthermore, unlike in the PC9 GR cells, EGFR inhibition does not lead to BIM induction or apoptosis in the PC9 GWR cells. Genomic analyses of the PC9 GWR compared with the PC9 GR cells, using single nucleotide polymorphism (SNP) arrays, identify a focal amplification in the PC9 GWR cells on chromosome 22 which includes ERK2 (MAP2K). Using fluorescence in situ hybridization (FISH), we confirm amplified intra-chromosomal regions mapping to MAP2K. Inhibition of ERK signaling by either an ERK2 specific shRNA or by the MEK inhibitor CI-1040, restores sensitivity to WZ4002 and BIBW2992. In addition, combination of WZ4002 and CI-1040 results in BIM induction and apoptosis in the PC9 GWR cells. In contrast inhibition of PI3K signaling using the PI3K inhibitor PI-103 does not restore WZ4002 sensitivity. Ectopic activation of ERK signaling using an activated MEK1 allele (MEK K57N) found in lung cancer, in different lung cancer cell lines (PC9 (EGFR del E746_A750), PC9 GR (EGFR del E746_A750), and H1975 (L858R/T790M), is sufficient to cause resistance to WZ4002 and block WZ4002 mediated apoptosis.

Conclusions: We identify amplification of ERK2, a component downstream component of EGFR signaling, as a mechanism of resistance to structurally distinct irreversible EGFR kinase inhibitors. The combination of an EGFR inhibitor and a MEK inhibitor is effective in against these drug resistant cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4736. doi:10.1158/1538-7445.AM2011-4736

Discovery of selective irreversible inhibitors for EGFR-T790M

Targeting the epidermal growth factor receptor kinase (EGFR) with ATP-competitive kinase inhibitors results in dramatic but short-lived responses in patients with EGFR mutant non small cell lung cancer. A series of novel covalent EGFR kinase inhibitors with selectivity for the clinically relevant T790M 'gatekeeper' resistance mutation relative to wild-type EGFR were discovered by library screening. A representative compound 3i was obtained through a systematic SAR study guided by mutant EGFR-dependent cellular proliferation assays.

Amplification of EGFR T790M causes resistance to an irreversible EGFR inhibitor

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors, gefitinib and erlotinib are effective therapies against mutant non-small cell lung cancers (NSCLCs). Treatment is limited by the development of resistance in part explained by the gain of a secondary EGFR mutation, T790M, at the gatekeeper residue. Irreversible EGFR inhibitors, including PF00299804, are effective in vitro and in vivo against EGFR mutant tumors that contain EGFR T790M and are currently under clinical development. In this study, we generate models of resistance to PF00299804, using cell lines with EGFR T790M and show that the PF00299804-resistant models develop focal amplification of EGFR that preferentially involves the T790M-containing allele. These PF00299804-resistant cell lines remain dependent on EGFR for growth as downregulation of EGFR by shRNA compromises their viability. We show that resistance to PF00299804 arises, at least in part, through selection of a pre-existing EGFR T790M-amplified clone both in vitro and using a xenograft model in vivo. Our findings show that EGFR T790M is a common resistance mechanism to both reversible, and when amplified, the irreversible EGFR kinase inhibitors further emphasizing the need to develop more potent therapies against EGFR T790M. These findings can be used to guide studies of patient tumor specimens from ongoing clinical trials of irreversible EGFR kinase inhibitors.

Abstract 1574: The impact of human wild type EGFR on lung tumorigenesis and in vivo sensitivity to EGFR-targeted therapies

Lung cancer is the leading cause of the cancer related death in the world. Non-small cell lung cancer is the major lung cancer type, of which more than 1.4 million new cases were diagnosed each year. Overexpression of wild type EGFR is common in NSCLC. However, it is not clear whether or not overexpression of wt EGFR is tumorigenic. We recently showed that overexpression of wt-hEGFR is capable of transforming cell lines. More importantly, inducible double transgenic mice overexpressing wt-hEGFR in lung epithelial compartment developed poorly differentiated lung adenocarcinoma and that the maintenance of the tumor is dependent on continuous functioning of wt-hEGFR. The tumor driven by overexpression of wt-hEGFR responds to cetuximab and erlotinib treatment.

These data suggest that a subpopulation of the lung cancer may be caused by overexpression of wt-hEGFR and that these lung cancers can be treated with anti-EGFR antibodies and EGFR tyrosine kinase inhibitors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1574.