Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach

Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.

Abstract 752: Elucidating the mechanisms of acquired resistance in lung adenocarcinomas

In EGFR mutant lung adenocarcinomas, targeted therapy with the EGFR tyrosine kinase inhibitors (TKIs) erlotinib, gefitinib, and afatinib performs better than standard chemotherapy in terms of progression free survival (PFS) and radiographic response (RR) rates. In the ALK rearranged cases, targeted therapy with crizotinib is associated with PFS of about 9,7 months and RR of 60.8%. Unfortunately, all patients relapse with a median PFS of 7 to 16 months. The mechanisms of acquired resistance to first generation EGFR TKIs include a secondary EGFR mutation (T790M) in about 50% and, with less frequency, MET amplification, HER2 amplification, PTEN loss, transformation to small cell histology, EMT and rare mutations in BRAF and PI3KCA. Resistance to crizotinib is caused by ALK kinase mutations, by ALK or cKIT amplification or by alterations in IGF1R/IRS1, EGFR and KRAS. Here, we made use of next generation sequencing techniques to better understand the mechanisms that drive resistance in lung adenocarcinomas treated with erlotinib or crizotinib. To this aim, we used rebiopsy samples from patients that had either prolonged stable disease or partial response to therapy, and developed radiographic progression under TKI therapy. To model the emergence of resistance mechanisms in vitro, we generated resistant cell lines to a variety of ALK inhibitors. Patient samples and resistant cell lines that were negative for any of the previously reported mechanisms of resistance were analyzed by genome or exome; validation of mutation calls was performed by Sanger sequencing. Sequencing of the erlotinib resistant samples revealed a deletion in the transmembrane domain of ABCD4, an ATP-binding cassette (ABC) transporter. Stable transduction of this mutation in BaF3 cells, showed that neither the expression of ABCD4 nor the mutation resulted in a reduced sensitivity to erlotinib. Results of the functional validation of a mutation found in a Fms-related tyrosine kinase are currently ongoing. Crizotinib resistant samples showed a mutation in the IPT/TIG domain of the RON kinase that, when expressed in sensitive cells, did not confer resistance to crizotinib. However, a mutation in the PSI domain of the semaphorin SEMA3E lead to an prologned Akt activation, thus sustained downstream PI3K signaling in cells treated with crizotinib. The molecular mechanisms behind this finding are being analyzed. Crizotinib resistant samples also showed mutations in SWI/SNF-regulator of chromatin and a GTPase of the Rab family. Cells resistant to different ALK inhibitors harbor mutations in a mitogen activated protein kinase and an ephrin receptor, among others. The functional impact of such mutations and the efficacy of combination therapies in the setting of resistance to these inhibitors are currently being tested. Our results imply a wide range of cellular pathways might be involved in the process of acquired resistance to EGFR and ALK inhibitors in lung adenocarcinomas.

Citation Format: Sandra Ortiz-Cuarán, Lynnette Fernandez-Cuesta, Christine M. Lovly, Marc Bos, Matthias Scheffler, Sebastian Michels, Kerstin Albus, Lydia Meyer, Katharina König, Ilona Dahmen, Christian Mueller, Luca Ozretić, Lars Tharun, Philipp Schaub, Alexandra Florin, Berit Pinther, Nike Bahlmann, Sascha Ansén, Martin Peifer, Lukas C. Heukamp, Reinhard Buettner, Martin L. Sos, Jürgen Wolf, William Pao, Roman K. Thomas. Elucidating the mechanisms of acquired resistance in lung adenocarcinomas. [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 752. doi:10.1158/1538-7445.AM2015-752

Abstract LB-210: Telomerase activation by genomic rearrangements in high-risk neuroblastoma

Neuroblastoma is a malignant pediatric tumor of the sympathetic nervous system. While roughly half of these tumors regress spontaneously or are cured by limited therapy, high-risk neuroblastomas have an unfavorable clinical course, despite intensive multimodal treatment. The genetic basis of the various clinical subtypes of the disease has remained largely elusive. To gain a better understanding of the genetic events that may drive neuroblastoma tumorigenesis, we here performed whole-genome sequencing of 42 primary neuroblastomas (high-risk, n = 25; low-risk, n = 17). We identified genomic rearrangements affecting chromosome 5p15.22 in a 50 kb region centromeric of the human telomerase reverse transcriptase gene (TERT) in 8 tumors. The rearrangements occurred only in high-risk neuroblastomas (8/25, 32%) in mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumor type. In an Independent validation cohort of 14 high-risk neuroblastomas, we detected rearrangements of the TERT locus in 4 additional samples. The structure of the rearrangements varied greatly, including balanced translocations, low-level copy number gains, focal amplifications and chromothripsis. Independent of the copy number at this region, all alterations consistently induced massive transcriptional up-regulation of TERT and of three additional genes located in close proximity to the chromosomal breakpoint. By contrast, MYCN-amplified tumors showed only up-regulation of TERT itself, suggesting that both MYCN amplification and TERT rearrangements converge on TERT activation. Supporting a functional role of TERT, both MYCN-amplified neuroblastoma cell lines and cell lines bearing TERT rearrangements exhibited elevated TERT expression and enzymatic telomerase activity in comparison to cell lines without these aberrations. Our findings show that remodeling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma, and places telomerase activation in the center of transformation in a large fraction of these tumors. More broadly, our findings provide a mechanistic basis for molecular diagnosis and therapy of this deadly pediatric tumor entity.

Citation Format: Martin Peifer, Frederik Roels, Falk Hertwig, Roopika Menon, Andrea Kraemer, Reinhard Buettner, Sven Perner, Alexander Schramm, Johannes H. Schulte, Frank Westermann, Roman K. Thomas, Matthias Fischer. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. [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-210. doi:10.1158/1538-7445.AM2015-LB-210

Comprehensive genomic profiles of small cell lung cancer

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.

A new generation of cancer genome diagnostics for routine clinical use: overcoming the roadblocks to personalized cancer medicine

The identification of 'druggable' kinase gene alterations has revolutionized cancer treatment in the last decade by providing new and successfully targetable drug targets. Thus, genotyping tumors for matching the right patients with the right drugs have become a clinical routine. Today, advances in sequencing technology and computational genome analyses enable the discovery of a constantly growing number of genome alterations relevant for clinical decision making. As a consequence, several technological approaches have emerged in order to deal with these rapidly increasing demands for clinical cancer genome analyses. Here, we describe challenges on the path to the broad introduction of diagnostic cancer genome analyses and the technologies that can be applied to overcome them. We define three generations of molecular diagnostics that are in clinical use. The latest generation of these approaches involves deep and thus, highly sensitive sequencing of all therapeutically relevant types of genome alterations-mutations, copy number alterations and rearrangements/fusions-in a single assay. Such approaches therefore have substantial advantages (less time and less tissue required) over PCR-based methods that typically have to be combined with fluorescence in situ hybridization for detection of gene amplifications and fusions. Since these new technologies work reliably on routine diagnostic formalin-fixed, paraffin-embedded specimens, they can help expedite the broad introduction of personalized cancer therapy into the clinic by providing comprehensive, sensitive and accurate cancer genome diagnoses in 'real-time'.

Crizotinib therapy for advanced lung adenocarcinoma and a ROS1 rearrangement: results from the EUROS1 cohort

PURPOSE

Approximately 1% of lung adenocarcinomas are driven by oncogenic ROS1 rearrangement. Crizotinib is a potent inhibitor of both ROS1 and ALK kinase domains.

PATIENTS AND METHODS

In the absence of a prospective clinical trial in Europe, we conducted a retrospective study in centers that tested for ROS1 rearrangement. Eligible patients had stage IV lung adenocarcinoma, had ROS1 rearrangement according to fluorescent in situ hybridization, and had received crizotinib therapy through an individual off-label use. Best response was assessed locally using RECIST (version 1.1). All other data were analyzed centrally.

RESULTS

We identified 32 eligible patients. One patient was excluded because next-generation sequencing was negative for ROS1 fusion. Median age was 50.5 years, 64.5% of patients were women, and 67.7% were never-smokers. Thirty patients were evaluable for progression-free survival (PFS), and 29 patients were evaluable for best response. We observed four patients with disease progression, two patients with stable disease, and objective response in 24 patients, including five complete responses (overall response rate, 80%; disease control rate, 86.7%). Median PFS was 9.1 months, and the PFS rate at 12 months was 44%. No unexpected adverse effects were observed. Twenty-six patients received pemetrexed (either alone or in combination with platinum and either before or after crizotinib) and had a response rate of 57.7% and a median PFS of 7.2 months.

CONCLUSION

Crizotinib was highly active at treating lung cancer in patients with a ROS1 rearrangement, suggesting that patients with lung adenocarcinomas should be tested for ROS1. Prospective clinical trials with crizotinib and other ROS1 inhibitors are ongoing or planned.

Identification and further development of potent TBK1 inhibitors

The cytosolic Ser/Thr kinase TBK1 was discovered to be an essential element in the mediation of signals that lead to tumor migration and progression. These findings meet the need for the identification of novel tool compounds and potential therapeutics to gain deeper insights into TBK1 related signaling and its relevance in tumor progression. Herein, we undertake the activity-based screening for unique inhibitors of TBK1 and their subsequent optimization. Initial screening approaches identified a selection of TBK1 inhibitors that were optimized using methods of medicinal chemistry. Variations of the structural characteristics of a representative 2,4,6-substituted pyrimidine scaffold resulted in improved potency. Prospective use as tool compounds or basic contributions to drug design approaches are anticipated for our improved small molecules.

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

Abstract 1690: Attacking EGFR mutant lung cancer by combined EGFR and c-Met inhibition

In lung adenocarcinomas, targeted therapy with the EGFR tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib is associated with longer progression free survival (PFS). However, despite the initial success, all patients progress with a median PFS of 12 to 16 months. Acquired resistance is driven by the occurrence of a secondary EGFR mutation (T790M) in about 50% of the cases and by c-Met amplification in 5 to 10 % of the cases. We report the activity of a new reversible and ATP-competitive c-Met inhibitor, EMD1214063, in the setting of primary lung adenocarcinomas harboring EGFR activating mutations and in two models of acquired resistance. EMD1214063 showed to be specifically active in c-Met amplified and c-Met dependent cells in a large panel of genotypically characterized lung cancer cell lines. In the context of acquired resistance, we studied the effect of EMD1214063 alone and in combination of afatinib, an irreversible EGFR TKI, in PC9 cells (EGFR Exon19del), H1975 cells (EGFR L858R and T790M), HCC827 (EGFR Exon19del, not c-Met amplified) and in HCC827GR cells (EGFR Exon19del and c-Met amplified). Treatment of HCC827GR cells with EMD1214063 resulted in substantial growth inhibition and induced apoptosis. The in vitro results showed a significant synergistic effect of the combination of EMD121039 and afatinib in the induction of growth inhibition in the context of c-Met amplification and EGFR T790M mutation. Combination treatment robustly suppressed expression of downstream pErk and pAkt, showing efficient suppression of PI3K and MAPK signaling. To determine whether the antitumor activity of the combination observed in vitro might also be apparent in vivo, we injected these cells in nude mice to elicit the formation of solid tumors. Mice were treated with EMD121043 (25mg/kg), afatinib (10mg/kg) or the combination of both. In H1975 xenografts only the combination therapy could significantly reduce tumor growth, thus confirming the results obtained in vitro. In the c-Met amplified setting, we treated mice harboring HCC827, HCC827GR and mixed xenografts. HCC827-driven tumors strongly responded to both afatinib monotherapy and to the combination, leading to complete remission within 40 days of therapy. HCC827/HCC827GR mixed xenografts containing 0.1%, 1% and 10% of HCC827GR cells partially responded to afatinib monotherapy; however, growth was completely abolished by combination therapy. Treatment with EMD1214063 led to significant growth reduction in mice harboring HCC827GR tumors. In this model, only the combination therapy led to massive tumor shrinkage. Assessment of cell proliferation in vivo by [18F]FLT-PET showed a decline in FLT-uptake of 40% in both the combination therapy and the EMD1214063 monotherapy. In conclusion, the combination of EMD1214063 and afatinib promote tumor regression in erlotinib acquired resistant lung cancers driven by EGFR L858R/T790M or EGFR Exon19 del/c-Met amplification.

Citation Format: Sandra Ortiz-Cuarán, Jakob Schöttle, Ilona Dahmen, Martin Peifer, Caroline Wieczoreck, Mirjam Koker, Michaela A. Ihle, Alexandra Florin, Berit Pinther, Lukas C. Heukamp, Roland T. Ullrich, Roman K. Thomas. Attacking EGFR mutant lung cancer by combined EGFR and c-Met inhibition. [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 1690. doi:10.1158/1538-7445.AM2014-1690

Abstract 956: Elucidating the mechanisms of acquired resistance in lung adenocarcinomas

In lung adenocarcinomas, targeted therapy with the EGFR tyrosine kinase inhibitors (TKIs) erlotinib, gefitinib and afatinib is associated with longer progression free survival (PFS) and higher radiographic response (RR) rates when compared to standard first-line chemotherapy. In ALK rearranged lung cancers, targeted therapy with crizotinib is associated with PFS of approximately 9,7 months and RR of 60.8%. However, despite the initial success of these agents, all patients progress with a median PFS of 7 to 16 months. Acquired resistance in EGFR mutant tumors is driven by the occurrence of a secondary EGFR mutation (T790M) in about 50% of the cases and by MET amplification in 5 to 10 % of the cases. Other mechanisms include HER2 amplification, PTEN loss, phenotypic change to small cell histology, rare mutations in BRAF and AXL activation. Resistance to crizotinib, on the other hand, is caused by secondary mutations in the ALK kinase domain, by ALK or cKIT amplification or by alterations in EGFR and KRAS. Here, we made use of next generation sequencing techniques to better understand the mechanisms that drive resistance in lung adenocarcinomas treated with erlotinib or crizotinib. For this purpose, we used transbronchial or CT-guided rebiopsies from patients that had either prolonged stable disease or partial response to therapy, and developed radiographic progression under TKI therapy. Samples were analyzed by FISH and sequenced on a benchtop Illumina platform (MiSeq) in order to evaluate the presence of known mechanisms of resistance. Samples that were negative for any of the reported mechanisms were analyzed by genome, exome or trascriptome sequencing. From the sequencing output of the pan-negative samples, filtering of mutation candidates included: absence of the mutation in the pre-treatment sample (when available), expression of the candidate gene in lung adenocarcinomas, absence of the mutation in primary lung adenocarcinomas, high impact of the mutation at protein level (Polyphen), mutant allelic fraction in the tumor higher than 10%, among other factors. After filtering, validation of mutation calls was performed by Sanger sequencing. Sequencing of the erlotinib resistant samples revealed mutations in members of a functionally wide spectrum of protein families including the proteoglycan family, the ATP-binding cassette (ABC) transporters family, an Fms-related tyrosine kinase receptor and a member of the transforming growth factor beta family of cytokines. On the other hand, crizotinib resistant samples showed mutations in a cell surface receptor for macrophage-stimulating protein with tyrosine kinase activity, in a C2H2 type zinc finger gene, a semaphorin, a mitogen-activated protein kinase and a member of the SWI/SNF family of proteins. Our results evidence the possible contribution of a wide range of cellular pathways in the process of acquired resistance to EGFR and ALK inhibitors in lung adenocarcinomas.

Citation Format: Sandra Ortiz-Cuarán, Lynnette Fernandez-Cuesta, Marc Bos, Lukas Heukamp, Christine M. Lovly, Martin Peifer, Masyar Gardizi, Matthias Scheffler, Ilona Dahmen, Christian Müller, Katharina König, Kerstin Albus, Alexandra Florin, Sascha Ansén, Reinhard Buettner, Jürgen Wolf, William Pao, Roman K. Thomas. Elucidating the mechanisms of acquired resistance in lung adenocarcinomas. [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 956. doi:10.1158/1538-7445.AM2014-956

Abstract 441: Functional characterization of recurrent CD74-NRG1 fusions in lung adenocarcinoma

In nearly 50% of all lung adenocarcinomas the oncogenic driver is still unknown. We performed transcriptome sequencing on 25 pan-negative lung adenocarcinomas of never smokers leading to the identification of the novel CD74-NRG1 gene fusion. In an additional cohort of 102 adenocarcinomas we could identify and validate four additional cases bearing the CD74-NRG1 fusion gene - all of the invasive mucinous subtype.

We then transduced NIH-3T3 cells with the fusion and found it localized on the cell surface in FACS experiments. As we found the identical breakpoint in CD74 in our fusion as in CD74-ROS1, we hypothesized that the functional active part needs to be NRG1. (Soda et al. 2012) The NRG1 isoform III-β3 that we found is generally not expressed in lung tissue - therefore the CD74 part leads to the expresseion of NRG1 III-β3 in the lung. As Neuregulins are known interaction partners of HER receptor family members we transduced the human adenocarcinoma cell lines H322 and H1568, that are HER receptor and KRAS wildtype, with the fusion and found phosphorylation of HER2 and HER3 in the transduced cells under starvation conditions compared to empty vector controls. (Hobbs et al. 2002) This holds true as well in the patient situation in which phospho-HER3 was only found in tumors expressing the fusion (p<0.0001).

We could further show that the CD74-NRG1 fusion is associated with activation of the phosphoinsitide-3-kinase pathway activation and the mitogen-activated protein (MAP) kinase pathway . As functional consequence we could observe in several human adenocarcinoma cell lines increased colony forming ability in soft-agar assays showing the CD74-NRG1 fusion being a new oncogenic driver in lung adenocarcinoma. This finding may lead to new treatment options for patients harboring this fusion gene who do not benefit from any effective treatment option up to now.

Citation Format: Dennis Plenker, Lynnette Fernandez-Cuesta, Hirotaka Osada, Ruping Sun, Marc Bos, Juliane Daßler, Gavin Wright, Elisabeth Brambilla, Reinhard Büttner, Sascha Ansen, Stefan Haas, Yasushi Yatabe, Roman K. Thomas. Functional characterization of recurrent CD74-NRG1 fusions in lung adenocarcinoma. [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 441. doi:10.1158/1538-7445.AM2014-441

Rationale for co-targeting IGF-1R and ALK in ALK fusion-positive lung cancer

Crizotinib, a selective tyrosine kinase inhibitor (TKI), shows marked activity in patients whose lung cancers harbor fusions in the gene encoding anaplastic lymphoma receptor tyrosine kinase (ALK), but its efficacy is limited by variable primary responses and acquired resistance. In work arising from the clinical observation of a patient with ALK fusion-positive lung cancer who had an exceptional response to an insulin-like growth factor 1 receptor (IGF-1R)-specific antibody, we define a therapeutic synergism between ALK and IGF-1R inhibitors. Similar to IGF-1R, ALK fusion proteins bind to the adaptor insulin receptor substrate 1 (IRS-1), and IRS-1 knockdown enhances the antitumor effects of ALK inhibitors. In models of ALK TKI resistance, the IGF-1R pathway is activated, and combined ALK and IGF-1R inhibition improves therapeutic efficacy. Consistent with this finding, the levels of IGF-1R and IRS-1 are increased in biopsy samples from patients progressing on crizotinib monotherapy. Collectively these data support a role for the IGF-1R-IRS-1 pathway in both ALK TKI-sensitive and ALK TKI-resistant states and provide a biological rationale for further clinical development of dual ALK and IGF-1R inhibitors.

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids

Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n=44) and transcriptome (n=69) sequencing of pulmonary carcinoids and observe frequent mutations in chromatin-remodelling genes. Covalent histone modifiers and subunits of the SWI/SNF complex are mutated in 40 and 22.2% of the cases, respectively, with MEN1, PSIP1 and ARID1A being recurrently affected. In contrast to small-cell lung cancer and large-cell neuroendocrine lung tumours, TP53 and RB1 mutations are rare events, suggesting that pulmonary carcinoids are not early progenitor lesions of the highly aggressive lung neuroendocrine tumours but arise through independent cellular mechanisms. These data also suggest that inactivation of chromatin-remodelling genes is sufficient to drive transformation in pulmonary carcinoids.

CD74-NRG1 fusions in lung adenocarcinoma

We discovered a novel somatic gene fusion, CD74-NRG1, by transcriptome sequencing of 25 lung adenocarcinomas of never smokers. By screening 102 lung adenocarcinomas negative for known oncogenic alterations, we found four additional fusion-positive tumors, all of which were of the invasive mucinous subtype. Mechanistically, CD74-NRG1 leads to extracellular expression of the EGF-like domain of NRG1 III-β3, thereby providing the ligand for ERBB2-ERBB3 receptor complexes. Accordingly, ERBB2 and ERBB3 expression was high in the index case, and expression of phospho-ERBB3 was specifically found in tumors bearing the fusion (P < 0.0001). Ectopic expression of CD74-NRG1 in lung cancer cell lines expressing ERBB2 and ERBB3 activated ERBB3 and the PI3K-AKT pathway, and led to increased colony formation in soft agar. Thus, CD74-NRG1 gene fusions are activating genomic alterations in invasive mucinous adenocarcinomas and may offer a therapeutic opportunity for a lung tumor subtype with, so far, no effective treatment.

SIGNIFICANCE

CD74–NRG1 fusions may represent a therapeutic opportunity for invasive mucinous lung adenocarcinomas, a tumor with no effective treatment that frequently presents with multifocal unresectable disease.

CGARS: cancer genome analysis by rank sums

MOTIVATION

Cancer genomes are characterized by the accumulation of point mutations and structural alterations such as copy-number alterations and genomic rearrangements. Among structural changes, systematic analyses of copy-number alterations have provided deeper insight into the architecture of cancer genomes and had led to new potential treatment opportunities. During the course of cancer genome evolution, selection mechanisms are leading to a non-random pattern of mutational events contributing to fitness benefits of the cancer cells. We therefore developed a new method to dissect random from non-random patterns in copy-number data and thereby to assess significantly enriched somatic copy-number aberrations across a set of tumor specimens or cell lines. In contrast to existing approaches, the method is invariant to any strictly monotonous transformation of the input data which results to an insensitivity of differences in tumor purity, array saturation effects and copy-number baseline levels.

RESULTS

We applied our approach to recently published datasets of small-cell lung cancer and squamous cell lung cancer and validated its performance by comparing the results to an orthogonal approach. In addition, we found a new deletion peak containing the HLA-A gene in squamous cell lung cancer.

Cell-autonomous and non-cell-autonomous mechanisms of transformation by amplified FGFR1 in lung cancer

The 8p12 locus (containing the FGFR1 tyrosine kinase gene) is frequently amplified in squamous cell lung cancer. However, it is currently unknown which of the 8p12-amplified tumors are also sensitive to fibroblast growth factor receptor (FGFR) inhibition. We found that, in contrast with other recurrent amplifications, the 8p12 region included multiple centers of amplification, suggesting marked genomic heterogeneity. FGFR1-amplified tumor cells were dependent on FGFR ligands in vitro and in vivo. Furthermore, ectopic expression of FGFR1 was oncogenic, which was enhanced by expression of MYC. We found that MYC was coexpressed in 40% of FGFR1-amplified tumors. Tumor cells coexpressing MYC were more sensitive to FGFR inhibition, suggesting that patients with FGFR1-amplified and MYC-overexpressing tumors may benefit from FGFR inhibitor therapy. Thus, both cell-autonomous and non-cell-autonomous mechanisms of transformation modulate FGFR dependency in FGFR1-amplified lung cancer, which may have implications for patient selection for treatment with FGFR inhibitors.

SIGNIFICANCE

Amplification of FGFR1 is one of the most frequent candidate targets in lung cancer. Here, we show that multiple factors affect the tumorigenic potential of FGFR1, thus providing clinical hypotheses for refinement of patient selection.

Tumor VEGF:VEGFR2 autocrine feed-forward loop triggers angiogenesis in lung cancer

The molecular mechanisms that control the balance between antiangiogenic and proangiogenic factors and initiate the angiogenic switch in tumors remain poorly defined. By combining chemical genetics with multimodal imaging, we have identified an autocrine feed-forward loop in tumor cells in which tumor-derived VEGF stimulates VEGF production via VEGFR2-dependent activation of mTOR, substantially amplifying the initial proangiogenic signal. Disruption of this feed-forward loop by chemical perturbation or knockdown of VEGFR2 in tumor cells dramatically inhibited production of VEGF in vitro and in vivo. This disruption was sufficient to prevent tumor growth in vivo. In patients with lung cancer, we found that this VEGF:VEGFR2 feed-forward loop was active, as the level of VEGF/VEGFR2 binding in tumor cells was highly correlated to tumor angiogenesis. We further demonstrated that inhibition of tumor cell VEGFR2 induces feedback activation of the IRS/MAPK signaling cascade. Most strikingly, combined pharmacological inhibition of VEGFR2 (ZD6474) and MEK (PD0325901) in tumor cells resulted in dramatic tumor shrinkage, whereas monotherapy only modestly slowed tumor growth. Thus, a tumor cell-autonomous VEGF:VEGFR2 feed-forward loop provides signal amplification required for the establishment of fully angiogenic tumors in lung cancer. Interrupting this feed-forward loop switches tumor cells from an angiogenic to a proliferative phenotype that sensitizes tumor cells to MAPK inhibition.