Transcriptomics and Transposon Mutagenesis Identify Multiple Mechanisms of Resistance to the FGFR Inhibitor AZD4547

In human cancers, FGFR signaling is frequently hyperactivated by deregulation of FGF ligands or by activating mutations in the FGFR receptors such as gene amplifications, point mutations, and gene fusions. As such, FGFR inhibitors are considered an attractive therapeutic strategy for patients with mutations in FGFR family members. We previously identified Fgfr2 as a key driver of invasive lobular carcinoma (ILC) in an in vivo insertional mutagenesis screen using the Sleeping Beauty transposon system. Here we explore whether these FGFR-driven ILCs are sensitive to the FGFR inhibitor AZD4547 and use transposon mutagenesis in these tumors to identify potential mechanisms of resistance to therapy. Combined with RNA sequencing-based analyses of AZD4547-resistant tumors, our in vivo approach identified several known and novel potential resistance mechanisms to FGFR inhibition, most of which converged on reactivation of the canonical MAPK-ERK signaling cascade. Observed resistance mechanisms included mutations in the tyrosine kinase domain of FGFR2, overexpression of MET, inactivation of RASA1, and activation of the drug-efflux transporter ABCG2. ABCG2 and RASA1 were identified only from de novo transposon insertions acquired during AZD4547 treatment, demonstrating that insertional mutagenesis in mice is an effective tool for identifying potential mechanisms of resistance to targeted cancer therapies.Significance: These findings demonstrate that a combined approach of transcriptomics and insertional mutagenesis in vivo is an effective method for identifying potential targets to overcome resistance to therapy in the clinic. Cancer Res; 78(19); 5668-79. ©2018 AACR.

Abstract IA06: Driver mutations and cell-of-origin as critical factors determining the phenotypic characteristics of thoracic tumor subtypes

We have generated mouse models for specific lung tumors and mesothelioma. These were based on the conditional somatic (in)activation of tumor suppressor genes and oncogenes. By using viruses driving Cre recombinase from specific promoters, we could achieve both sporadic and cell-type specific switching of the conditional alleles allowing us to address the importance of the target cell in the development of specific tumor subtypes. We made the following observations.

Small cell lung cancer (SCLC) development was fully dependent on the inactivation of Rb in conjunction with loss of p53. This neuroendocrine tumor could be most efficiently induced by targeting neuroendocrine cells using an Ad5-CGRP-Cre virus. However, when Rb and p53 were inactivated in combination with overexpression of L-myc, a gene frequently found amplified in both human and mouse, we noted additional tumors with a more peripheral location (more precisely at the bronchiolar-alveolar junction region) and with a less aggressive phenotype, but only when these tumors were induced by an Ad5-CMV-Cre virus. Since the latter tumors were strongly positive for neuroendocrine markers including CGRP, this indicates that the latter tumor subtype originated from a cell with no or very low CGRP expression and therefore different from the neuroendocrine cell targeted by Ad5-CGRP-Cre. The cell type giving rise to this tumor is not yet defined. Nevertheless, the different phenotypic characteristics of this tumor—that shows many of the features of SCLC—likely also have consequences for its prognosis and response to therapy.

In testing a number of different combinations of lesions to induce squamous cell carcinoma (SCC), we found that development of SCC strongly depended on the overexpression of Sox2. Biallelic inactivation of Pten and Cdkn2a;Cdkn2b;p19Arf in combination with Sox2 overexpression promoted SCC at high penetrance but after a relatively long latency period. Phenotypically mouse SCC closely resembled human SCC, showing a very similar immunophenotyped, indicating that this is largely commanded by the tumor subtype. Interestingly, SCC could be induced at the same extend by activating the aforementioned genetic lesions in Basal, Club, and Alveolar type II cells (AT2). When targeting the latter two cell subtypes, they went through a dedifferentiation/transdifferentiation process with the concomitant loss and gain of transient cell markers; e.g., when targeting AT2 cells, the cells would lose SPC expression, transiently express the Club marker CC10, to acquire subsequently the biomarker of SCC, K5, and p63. Histopathology showed a process of transdifferentiation of the alveolar cells to Club cells and eventually to neoplastic squamous cells. Although the cell-of-origin did influence the extent of progression of individual tumor nodules (more small lesions upon induction of transformation of AT2 cells), the phenotypic characteristics of the tumors were very similar and could not be distinguished on basis of RNA expression.

In the case of adenocarcinomas developing in LSL-KrasG12D;p53f/f mice, the cell-of-origin did again influence the tumor phenotype. When Club cells were targeted, the cells would lose the Club cell specific marker expression (CC10 and Sox2) and acquire pronounced SPC expression while such changes were not seen upon targeting AT2 cells. They retained their SPC expression. However, the tumors induced in Club cells showed a more pronounced papillary phenotype as well as a more aggressive growth pattern as compared to tumors induced in AT2 cells.

A similar situation was encountered in mesothelioma. Although this tumor is less stringently dependent on the specific lesions, loss of Nf2 in conjunction with p53 pathway inactivation and Cdkn2a loss is an effective route to malignant mesothelioma (MM). MM development can be further accelerated by BAP1 loss resulting in an autochthonous model that is as fast as tumor graft models. Some of the advantageous and disadvantages of each will be discussed.

MM can manifest as three major subtypes: epithelioid, sarcomatoid, and biphasic. Each of those can be induced by the same set of mutations (loss-of-function of Nf2, p53, and Cdkn2a). The tumor subtype that arises depends on the cell-of-origin. The three subtypes exhibit relative stable phenotypes with the phenotypic appearance of the biphasic tumor depending on the microenvironmental cues. Changing those makes this subtype either more epithelioid or sarcomatoid.

The examples described show that both the combination of genetic lesion and the cell-of-origin are critical factors defining tumor characteristics. In some cases, targeting different cell types with the same lesions gives rise to seemingly indistinguishable tumors (e.g., SCC), whereas in other cases the same genetic lesions cause tumor features that are strongly influenced by the cell-of-origin (as is the case in MM and SCLC), emphasizing that the cell-of-origin might be an important factor that should be taken into account when designing intervention strategies within otherwise highly similar tumors.

Citation Format: Anton Berns, Ekaterina Semenova, Giustina Ferone, Hilda de Vries, Jitendra Badhai, Min-chul Kwon, Kate Sutherland, Lorenzo Bombardelli, Rajith Bhaskaran, Ji-Ying Song. Driver mutations and cell-of-origin as critical factors determining the phenotypic characteristics of thoracic tumor subtypes [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr IA06.

Rejuvenation by Therapeutic Elimination of Senescent Cells

In this issue of Cell, Baar et al. show how FOXO4 protects senescent cell viability by keeping p53 sequestered in nuclear bodies, preventing it from inducing apoptosis. Disrupting this interaction with an all-D amino acid peptide (FOXO4-DRI) restores p53's apoptotic role and ameliorates the consequences of senescence-associated loss of tissue homeostasis.

Awakening of "Schlafen11" to Tackle Chemotherapy Resistance in SCLC

Chemotherapy resistance arises invariably in small cell lung cancer (SCLC). In this issue of Cancer Cell, Gardner et al. find that in some SCLC, EZH2 mediates resistance via downregulation of Schlafen11 (SLFN11). Combining EZH2 inhibition with chemotherapy effectively overcomes drug resistance of xenografted SCLC, holding promise for new treatment paradigms.

SOX2 Is the Determining Oncogenic Switch in Promoting Lung Squamous Cell Carcinoma from Different Cells of Origin

Lung squamous cell carcinoma (LSCC) is a devastating malignancy with no effective treatments, due to its complex genomic profile. Therefore, preclinical models mimicking its salient features are urgently needed. Here we describe mouse models bearing various combinations of genetic lesions predominantly found in human LSCC. We show that SOX2 but not FGFR1 overexpression in tracheobronchial basal cells combined with Cdkn2ab and Pten loss results in LSCC closely resembling the human counterpart. Interestingly, Sox2;Pten;Cdkn2ab mice develop LSCC with a more peripheral location when Club or Alveolar type 2 (AT2) cells are targeted. Our model highlights the essential role of SOX2 in commanding the squamous cell fate from different cells of origin and represents an invaluable tool for developing better intervention strategies.

Drugging the addict: non-oncogene addiction as a target for cancer therapy

Historically, cancers have been treated with chemotherapeutics aimed to have profound effects on tumor cells with only limited effects on normal tissue. This approach was followed by the development of small‐molecule inhibitors that can target oncogenic pathways critical for the survival of tumor cells. The clinical targeting of these so‐called oncogene addictions, however, is in many instances hampered by the outgrowth of resistant clones. More recently, the proper functioning of non‐mutated genes has been shown to enhance the survival of many cancers, a phenomenon called non‐oncogene addiction. In the current review, we will focus on the distinct non‐oncogenic addictions found in cancer cells, including synthetic lethal interactions, the underlying stress phenotypes, and arising therapeutic opportunities.

Transcription Factor NFIB Is a Driver of Small Cell Lung Cancer Progression in Mice and Marks Metastatic Disease in Patients

Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor, and no effective treatment is available to date. Mouse models of SCLC based on the inactivation of Rb1 and Trp53 show frequent amplifications of the Nfib and Mycl genes. Here, we report that, although overexpression of either transcription factor accelerates tumor growth, NFIB specifically promotes metastatic spread. High NFIB levels are associated with expansive growth of a poorly differentiated and almost exclusively E-cadherin (CDH1)-negative invasive tumor cell population. Consistent with the mouse data, we find that NFIB is overexpressed in almost all tested human metastatic high-grade neuroendocrine lung tumors, warranting further assessment of NFIB as a tumor progression marker in a clinical setting.

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NFIB drives tumor initiation and progression in mouse models of SCLC

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NFIB enhances metastasis and changes the metastatic profile

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NFIB promotes dedifferentiation and invasion in SCLC

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NFIB marks stage III/IV high-grade neuroendocrine carcinomas in patients

Excellent translational research in oncology: A journey towards novel and more effective anti-cancer therapies

Comprehensive Cancer Centres (CCCs) serve as critical drivers for improving cancer survival. In Europe, we have developed an Excellence Designation System (EDS) consisting of criteria to assess "excellence" of CCCs in translational research (bench to bedside and back), with the expectation that many European CCCs will aspire to this status.

The steady progress of targeted therapies, promising advances for lung cancer

Lung cancer remains one of the most complex and challenging cancers, being responsible for almost a third of all cancer deaths. This grim picture seems however to be changing, for at least a subset of lung cancers. The number of patients who can benefit from targeted therapies is steadily increasing thanks to the progress made in identifying actionable driver lesions in lung tumours. The success of the latest generation of EGFR and ALK inhibitors in the clinic not only illustrates the value of targeted therapies, but also shows how almost inevitably drug resistance develops. Therefore, more sophisticated approaches are needed to achieve long-term remissions. Although there are still significant barriers to be overcome, technological advances in early detection of relevant mutations and the opportunity to test new drugs in predictive preclinical models justify the hope that we will overcome these obstacles.

Abstract IA05: Polycomb repressive complex-2 is a barrier to Kras-driven inflammation and epithelial-mesenchymal transition in non-small cell lung cancer

Polycomb repressive complexes (PRC) are frequently implicated in human cancer acting either as oncogenes or tumor suppressors. Here we show that PRC2 is a critical regulator of Kras-driven non-small-cell lung cancer (NSCLC) progression. Modulation of PRC2 by either Ezh2 overexpression or Eed deletion enhances Kras-driven adenomagenesis and inflammation, respectively. Eed-loss-driven inflammation leads to massive macrophage recruitment and marked decline in tissue function. Additional Trp53 inactivation activates a cell autonomous epithelial-to- mesenchymal transition (EMT) program leading to an invasive mucinous adenocarcinoma. A switch between methylated/acetylated chromatin underlies the tumor phenotypic evolution, prominently involving genes controlled by Hippo/Wnt-signaling. Our observations in the mouse models were conserved in human cells. Importantly, PRC2 inactivation results in context-dependent phenotypic alterations, with implications for its therapeutic application.

Citation Format: Michela Serresi, Gaetano Gargiulo, Nathalie Proost, Bjorn Siteur, Matteo Cesaroni, Martijn Koppens, Huafeng Xie, Kate Sutherland, Danielle Hulsman, Elisabetta Citterio, Stuart Orkin, Anton Berns, Maarten van Lohuizen. Polycomb repressive complex-2 is a barrier to Kras-driven inflammation and epithelial-mesenchymal transition in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference: Developmental Biology and Cancer; Nov 30-Dec 3, 2015; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(4_Suppl):Abstract nr IA05.

Human malignant mesothelioma is recapitulated in immunocompetent BALB/c mice injected with murine AB cells

Malignant Mesothelioma is a highly aggressive cancer, which is difficult to diagnose and treat. Here we describe the molecular, cellular and morphological characterization of a syngeneic system consisting of murine AB1, AB12 and AB22 mesothelioma cells injected in immunocompetent BALB/c mice, which allows the study of the interplay of tumor cells with the immune system. Murine mesothelioma cells, like human ones, respond to exogenous High Mobility Group Box 1 protein, a Damage-Associated Molecular Pattern that acts as a chemoattractant for leukocytes and as a proinflammatory mediator. The tumors derived from AB cells are morphologically and histologically similar to human MM tumors, and respond to treatments used for MM patients. Our system largely recapitulates human mesothelioma, and we advocate its use for the study of MM development and treatment.

Polycomb Repressive Complex 2 Is a Barrier to KRAS-Driven Inflammation and Epithelial-Mesenchymal Transition in Non-Small-Cell Lung Cancer

Polycomb repressive complexes (PRC) are frequently implicated in human cancer, acting either as oncogenes or tumor suppressors. Here, we show that PRC2 is a critical regulator of KRAS-driven non-small cell lung cancer progression. Modulation of PRC2 by either Ezh2 overexpression or Eed deletion enhances KRAS-driven adenomagenesis and inflammation, respectively. Eed-loss-driven inflammation leads to massive macrophage recruitment and marked decline in tissue function. Additional Trp53 inactivation activates a cell-autonomous epithelial-to-mesenchymal transition program leading to an invasive mucinous adenocarcinoma. A switch between methylated/acetylated chromatin underlies the tumor phenotypic evolution, prominently involving genes controlled by Hippo/Wnt signaling. Our observations in the mouse models were conserved in human cells. Importantly, PRC2 inactivation results in context-dependent phenotypic alterations, with implications for its therapeutic application.

Using the GEMM-ESC strategy to study gene function in mouse models

Preclinical in vivo validation of target genes for therapeutic intervention requires careful selection and characterization of the most suitable animal model in order to assess the role of these genes in a particular process or disease. To this end, genetically engineered mouse models (GEMMs) are typically used. However, the appropriate engineering of these models is often cumbersome and time consuming. Recently, we and others described a modular approach for fast-track modification of existing GEMMs by re-derivation of embryonic stem cells (ESCs) that can be modified by recombinase-mediated transgene insertion and subsequently used for the production of chimeric mice. This 'GEMM-ESC strategy' allows for rapid in vivo analysis of gene function in the chimeras and their offspring. Moreover, this strategy is compatible with CRISPR/Cas9-mediated genome editing. This protocol describes when and how to use the GEMM-ESC strategy effectively, and it provides a detailed procedure for re-deriving and manipulating GEMM-ESCs under feeder- and serum-free conditions. This strategy produces transgenic mice with the desired complex genotype faster than traditional methods: generation of validated GEMM-ESC clones for controlled transgene integration takes 9-12 months, and recombinase-mediated transgene integration and chimeric cohort production takes 2-3 months. The protocol requires skills in embryology, stem cell biology and molecular biology, and it is ideally performed within, or in close collaboration with, a transgenic facility.

Origins, genetic landscape, and emerging therapies of small cell lung cancer

Lung cancer is the leading cause of cancer deaths, with small cell lung cancer (SCLC) representing the most aggressive subtype. Standard treatments have not changed in decades, and the 5-year survival rate has remained <7%. Genomic analyses have identified key driver mutations of SCLC that were subsequently validated in animal models of SCLC. To provide better treatment options, a deeper understanding of the cellular and molecular mechanisms underlying SCLC initiation, progression, metastasis, and acquisition of resistance is required. In this review, we describe the genetic landscape of SCLC, features of the cell of origin, and targeted therapeutic approaches.

Wnt Down, Tumors Wind Up?

In mouse intestinal tumors induced by the inhibition of APC, the restoration of APC function causes complete tumor regression with normal differentiation and return of stem cell function irrespective of whether tumors also carried mutations in Kras and p53. These findings by Dow et al. validate the Wnt pathway as an exquisite target for intervention.

Abstract LB-201: Functional role for tumor heterogeneity: Paracrine signaling between tumor subclones of mouse SCLC promotes metastasis

Tumor heterogeneity might not only lead to pools of cells with a different resistance profile to therapy, the heterogeneity can also create a unique tumor-microenvironment. Earlier we have shown that clonal evolution in mouse SCLC can result in subclones with either neuro-endocrine (NE) and non-NE features. Co-grafting of such subclones endow the NE tumor cells with metastatic potential. To address the underlying mechanism we conducted a series of in vivo graft experiments and found that non-cell autonomous paracrine signaling is required in the subcutaneously grafted tumor to permit dissemination. The expression of transcription factor Pea3 in NE cells was identified as a functional downstream target of this paracrine interaction between the tumor subclones. Fgf2 secreted by non-NE subclones causes the expression of Pea3 in the NE cells through activation of Mapk pathway thereby temporarily potentiating its invasive capacity and facilitating intravasation into the circulation. These findings reveal a cooperating role of tumor cell subclones in mouse SCLC. Our data indicate that inhibition of the Fgf2/Mapk/Pea3 axis might be exploited to impair growth and metastatic spread of SCLC. Given the similarity in phenotypic tumor cell heterogenenity and signaling aberrations between mouse and human SCLC, inhibition of this signaling axis is therefore worth exploring in human SCLC.

Citation Format: Min Chul Kwon, Natalie Proost, Kate Sutherland, John Zevenhoven, Anton Berns. Functional role for tumor heterogeneity: Paracrine signaling between tumor subclones of mouse SCLC promotes metastasis. [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-201. doi:10.1158/1538-7445.AM2015-LB-201

Paracrine signaling between tumor subclones of mouse SCLC: a critical role of ETS transcription factor Pea3 in facilitating metastasis

Kwon et al. show that paracrine signaling between SCLC subclones is a critical requirement in the early steps of the metastatic process. Paracrine signaling via Fgf2 and MAPK between these diverged tumor subclones causes enhanced expression of the Pea3 transcription factor, resulting in metastatic dissemination of the neuroendocrine tumor subclones.

Tumor heterogeneity can create a unique symbiotic tumor microenvironment. Earlier, we showed that clonal evolution in mouse small cell lung cancer (SCLC) can result in subclones that, upon cografting, endow the neuroendocrine tumor cells with metastatic potential. We now show that paracrine signaling between SCLC subclones is a critical requirement in the early steps of the metastatic process, such as local invasion and intravasation. We further show evidence that paracrine signaling via fibroblast growth factor 2 (Fgf2) and Mapk between these diverged tumor subclones causes enhanced expression of the Pea3 (polyomavirus enhancer activator 3) transcription factor, resulting in metastatic dissemination of the neuroendocrine tumor subclones. Our data reveal for the first time paracrine signaling between tumor cell subclones in SCLC that results in metastatic spread of SCLC.