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Supplementary figure 4. Cell viability data based to generate the synergy plots in Figures 2 and 3.

Supplementary figure 1A. Sequencing tracks of a part of the Zwilch gene targeted by a first unique sgRNA, with the wildtype sequence (top) and sgRNA treated sequence (bottom) shown. B. Tide analysis showing editing efficiency of the first Zwilch targeting sgRNA

Supplementary figure 1C. Sequencing tracks of a part of the Zwilch gene targered by a second unique sgRNA, with the wildtype sequence (top) and sgRNA treated sequence (bottom) shown. D. Tide analysis showing editing efficiency of the second Zwilch targeting sgRNA

Small cell lung cancer (SCLC) is generally regarded as very difficult to treat, mostly due to the development of metastases early in the disease and a quick relapse with resistant disease. SCLC patients initially show a good response to treatment with the DNA damaging agents cisplatin and etoposide. This is, however, quickly followed by the development of resistant disease, which urges the development of novel therapies for this type of cancer. In this study, we set out to compile a comprehensive overview of the vulnerabilities of SCLC. A functional genome-wide screen where all individual genes were knocked out was performed to identify novel vulnerabilities of SCLC. By analysis of the knockouts that were lethal to these cancer cells, we identified several processes to be synthetic vulnerabilities in SCLC. We were able to validate the vulnerability to inhibition of the replication stress response machinery by use of Chk1 and ATR inhibitors. Strikingly, SCLC cells were more sensitive to these inhibitors than nontransformed cells. In addition, these inhibitors work synergistically with either etoposide and cisplatin, where the interaction is largest with the latter. ATR inhibition by VE-822 treatment in combination with cisplatin also outperforms the combination of cisplatin with etoposide in vivo. Altogether, our study uncovered a critical dependence of SCLC on the replication stress response and urges the validation of ATR inhibitors in combination with cisplatin in a clinical setting.

Supplementary figure 2. Graphs showing the correlation between all three replicates of the genome�wide CRISPR�Cas9 screen at the start of the experiment (t=0) and at the final time point (t=14).

Supplementary figure 3A and B. Graph representing the mRNA levels of MYC and MYCL1 in a panel of 63 human SCLC cell lines. Cut-offs for the analysis of low and high expressing cells were set as indicated. C. Graphs showing the 2log(IC50) for a selection of CHK1 and ATR inhibitors of a panel of 63 human SCLC cell lines screened by Polley at al. (21). Cell lines were grouped on the basis of absence or presence of either MYC or MYCL1 expression. D. p-values for testing between the MYC/MYCL1 low and either high group were calculated using a Mann- Whitney U test and were corrected for multiple testing using Benjamini-Hochberg.

Small cell lung cancer (SCLC) is generally regarded as very difficult to treat, mostly due to the development of metastases early in the disease and a quick relapse with resistant disease. SCLC patients initially show a good response to treatment with the DNA damaging agents cisplatin and etoposide. This is, however, quickly followed by the development of resistant disease, which urges the development of novel therapies for this type of cancer. In this study, we set out to compile a comprehensive overview of the vulnerabilities of SCLC. A functional genome-wide screen where all individual genes were knocked out was performed to identify novel vulnerabilities of SCLC. By analysis of the knockouts that were lethal to these cancer cells, we identified several processes to be synthetic vulnerabilities in SCLC. We were able to validate the vulnerability to inhibition of the replication stress response machinery by use of Chk1 and ATR inhibitors. Strikingly, SCLC cells were more sensitive to these inhibitors than nontransformed cells. In addition, these inhibitors work synergistically with either etoposide and cisplatin, where the interaction is largest with the latter. ATR inhibition by VE-822 treatment in combination with cisplatin also outperforms the combination of cisplatin with etoposide in vivo. Altogether, our study uncovered a critical dependence of SCLC on the replication stress response and urges the validation of ATR inhibitors in combination with cisplatin in a clinical setting.

Badhai et al. describe a mouse model of mesothelioma with combined deletion of Bap1, Nf2, and Cdkn2ab that shows rapid onset and recapitulates human mesothelioma including its response to the standard treatment. This autochthonous model is well suited for testing cancer immunotherapies., We have generated mouse models of malignant mesothelioma (MM) based upon disruption of the Bap1, Nf2, and Cdkn2ab tumor suppressor loci in various combinations as also frequently observed in human MM. Inactivation of all three loci in the mesothelial lining of the thoracic cavity leads to a highly aggressive MM that recapitulates the histological features and gene expression profile observed in human patients. The tumors also show a similar inflammatory phenotype. Bap1 deletion alone does not cause MM but dramatically accelerates MM development when combined with Nf2 and Cdkn2ab (hereafter BNC) disruption. The accelerated tumor development is accompanied by increased Polycomb repression and EZH2-mediated redistribution of H3K27me3 toward promoter sites with concomitant activation of PI3K and MAPK pathways. Treatment of BNC tumor–bearing mice with cisplatin and pemetrexed, the current frontline treatment, prolongs survival. This makes the autochthonous mouse model described here very well suited to explore the pathogenesis of MM and validate new treatment regimens for MM, including immunotherapy.

Summary Fibroblast growth factor receptor 1 (FGFR1) is frequently amplified in human small-cell lung cancer (SCLC), but its contribution to SCLC and other lung tumors has remained elusive. Here, we assess the tumorigenic capacity of constitutive-active FGFR1 (FGFR1K656E) with concomitant RB and P53 depletion in mouse lung. Our results reveal a context-dependent effect of FGFR1K656E: it impairs SCLC development from CGRPPOS neuroendocrine (NE) cells, which are considered the major cell of origin of SCLC, whereas it promotes SCLC and low-grade NE bronchial lesions from tracheobronchial-basal cells. Moreover, FGFR1K656E induces lung adenocarcinoma (LADC) from most lung cell compartments. However, its expression is not sustained in LADC originating from CGRPPOS cells. Therefore, cell context and tumor stage should be taken into account when considering FGFR1 inhibition as a therapeutic option., Graphical Abstract, Highlights • FGRF signaling impairs SCLC development initiated from CGRPPOS NE cells • FGRF signaling promotes development of NE tumors initiated from K14POS cells • Rb;p53;Fgfr1 mice develop ADCs that retain signatures of their cell of origin • Low expression of Fgfr1 in progressed tumors suggests a role in tumor initiation, Ferone et al. show that inducing FGFR signaling in lung neuroendocrine (NE) cells of Rb;p53 mice results in impairment of SCLC and enhancement of peripheral NE lesions. The location and tumor characteristics depend on the targeted cell type. Rb;p53;Fgfr1 mice also develop adenocarcinomas with the incidence depending on the targeted cell type.

Human cancers modeled in Genetically Engineered Mouse Models (GEMMs) can provide important mechanistic insights into the molecular basis of tumor development and enable testing of new intervention strategies. The inherent complexity of these models, with often multiple modified tumor suppressor genes and oncogenes, has hampered their use as preclinical models for validating cancer genes and drug targets. In our newly developed approach for the fast generation of tumor cohorts we have overcome this obstacle, as exemplified for three GEMMs; two lung cancer models and one mesothelioma model. Three elements are central for this system; (i) The efficient derivation of authentic Embryonic Stem Cells (ESCs) from established GEMMs, (ii) the routine introduction of transgenes of choice in these GEMM-ESCs by Flp recombinase-mediated integration and (iii) the direct use of the chimeric animals in tumor cohorts. By applying stringent quality controls, the GEMM-ESC approach proofs to be a reliable and effective method to speed up cancer gene assessment and target validation. As proof-of-principle, we demonstrate that MycL1 is a key driver gene in Small Cell Lung Cancer.

Introduction Lung squamous cell carcinoma (LSCC) is a lethal disease accounting for 30% of all lung cancer cases. Currently, there are no effective treatments: patients are treated with a combination of surgery, chemotherapy and radiotherapy. So far numerous high-throughput screenings have been carried out in order to identify the representative mutations of this tumour. Their contribution is precious but remains descriptive. Material and methods Mice were engineered by using Flp-Recombinase mediated cassette exchange technology in ES cells. Mutations were activated by Intratracheal injection of adenoviruses carrying Cre recombinase under different promoters. Genome profiling and histological analysis were performed on lung isolated from mice that showed signs of distress due to tumour development. Results and discussions We published that mice carrying SOX2 over-expression combined with PTEN and CDKN2AB loss (hereafter SOX2PC) developed central and peripheral LSCC according to the targeted cell-of-origin, fully mimicking the human counterpart. To examine gene contribution, we uncoupled the inactivation of tumour suppressor genes and found that mice defective either of PTEN or CDKN2AB in combination with SOX2 over-expression, only showed epithelial hyperplasia, indicating that the combination is necessary for the tumour to progress. In order to use SOX2PC autochthonous model for intervention studies, we attempted at reducing tumour latency by combining other oncogenes with SOX2 over-expression. Our data pointed at FGFR1 and NFE2L2 as candidate drivers of human LSCC. Surprisingly, FGFR1-SOX2PC mice were resistant to tumour formation, indicating that FGFR1 downstream pathways may be detrimental to squamous differentiation. However, NFE2L2, a transcription factor involved in the anti-oxidant pathway and found altered in 12% of human LSCC cases, strongly enhanced tumour progression without affecting the overall tumour morphology. Most importantly, in both NFE2L2-SOX2PC and SOX2PC mice, we observed a highly immunogenic microenvironment, as reported for human patients, with high level of PD-L1 and extensive immune infiltrations of leukocytes mostly of myeloid lineage. Conclusion Our data show that neoplastic squamous differentiation is strongly associated to the oncogenic activation of SOX2. Concomitant activation of the anti-oxidant pathway accelerates tumour progression, making NFE2L2-SOX2PC autochthonous model, with its characteristic immunophenotype (massive myeloid immune infiltrations) suitable for a diversity of intervention studies.

Introduction Malignant mesothelioma(MM) is a highly aggressive tumour of serosal surfaces. The vast majority of cases of mesothelioma are linked to asbestos exposure. Loss of BAP1, NF2, and CDKN2ABtumour suppressor gene function is frequently observed in malignant mesothelioma. There is limited treatment option available with cisplatin/pemetrexed as the main frontline therapy with modest survival advantage. There is an urgent need of preclinical models that are fast, reproducible and that recapitulates human disease to test new treatment modalities. Here, we describe a mouse model of MM based upon the co-deletion of Bap1, Nf2, and Cdkn2ab. Material and methods Mesotheliomas were induced by deleting Bap1, Nf2, and Cdkn2ab in the thoracic cavity of mice. The tumour and its microenvironment were characterised histologically. Furthermore, we performed gene expression, chromatin profiling and drug response in tumor-derived primary cells. In addition, we employed this autochthonous model for testing current standard of care as a proof of concept treatment. Results and discussions The combined inactivation of Bap1, Nf2, and Cdkn2ab in thoracic cavity led to a highly aggressive primarily epithelioid mesothelioma with histopathological features and gene expression profile similar to human MM. This includes the distinct inflammatory phenotype. Bap1 deletion accelerated mesothelioma dramatically when combined with Nf2, Cdkn2a, Cdkn2b and p19Arf disruption (hereafter refer as BNC loss). The accelerated tumour development is invariably connected with EZH2 mediated redistribution of H2K27me3 towards promoter sites, and activation of the PI3K, MAPK pathway. The primary cells derived from mouse mesothelioma showed drug response profile similar to those observed in human MM. Treatment of BNC tumours with cisplatin and pemetrexed, the current frontline treatment modestly prolonged survival of the mice. Conclusion We have developed a mouse model that is fast and recapitulates human mesothelioma. The mouse model is an ideal model system to study the biology and pathogenesis of mesothelioma. Furthermore, the immune-competence of this model, and the fast and synchronous tumour onset makes it very suitable to design and validate new treatment regimens for this deadly disease.

Summary Small-cell lung cancer is the most aggressive type of lung cancer, characterized by a remarkable response to chemotherapy followed by development of resistance. Here, we describe SCLC subtypes in Mycl- and Nfib-driven GEMM that include CDH1-high peripheral primary tumor lesions and CDH1-negative, aggressive intrapulmonary metastases. Cisplatin treatment preferentially eliminates the latter, thus revealing a striking differential response. Using a combined transcriptomic and proteomic approach, we find a marked reduction in proliferation and metabolic rewiring following cisplatin treatment and present evidence for a distinctive metabolic and structural profile defining intrinsically resistant populations. This offers perspectives for effective combination therapies that might also hold promise for treating human SCLC, given the very similar response of both mouse and human SCLC to cisplatin., Graphical Abstract, Highlights • Heterogeneity and plasticity of SCLC underlies differential sensitivity to cisplatin • Cisplatin selectively eradicates the CDH1-negative, NFIB-positive SCLC compartment • Identification of intrinsically cisplatin-resistant CDH1-high alveolar lesions • Multi-omics analysis identifies distinctive metabolic circuitry in resistant populations, Böttger et al. show the presence of histologically and molecularly distinct sub-populations of small-cell lung cancer (SCLC) in advanced mouse models. They demonstrate that the heterogeneity of SCLC is responsible for the differential sensitivity to cisplatin and identify metabolic circuitries that likely contribute to cisplatin resistance.

During the past years, evidence accumulated showing that glycine comprises anti-inflammatory activities. These effects occur, at least in part, via the activation of glycine-gated chloride channels (GlyR). Glycine is one of the major structural units of collagen, making up about 30% of the amino acids. This study aims to investigate the anti-inflammatory potential of collagen hydrolysate (CH) using the zymosan-induced ear-skin inflammation mouse model. After oral intake of 12.5, 25 or 50 mg CH the plasma levels of glycine increased in a concentration-dependent manner. CH was able to counteract zymosan-induced ear-skin inflammation locally (ear swelling) as well as systemically (IL-6 production by lipopolysaccharide (LPS)-stimulated whole blood cells). The LPS-stimulated IL-6 production in whole blood correlated positively with the ear swelling response. This correlation was abolished by strychnine (a glycine receptor antagonist), indicating the involvement of GlyR. Collectively, these data show that CH is able to modulate inflammatory responses both locally as well as systemically. This effect might be constituted by inhibiting pro-inflammatory cytokine production via GlyR.

The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. It is currently believed that four to six crypt stem cells reside at the +4 position immediately above the Paneth cells in the small intestine; colon stem cells remain undefined. Lgr5 (leucine-rich-repeat-containing G-protein-coupled receptor 5, also known as Gpr49) was selected from a panel of intestinal Wnt target genes for its restricted crypt expression. Here, using two knock-in alleles, we reveal exclusive expression of Lgr5 in cycling columnar cells at the crypt base. In addition, Lgr5 was expressed in rare cells in several other tissues. Using an inducible Cre knock-in allele and the Rosa26-lacZ reporter strain, lineage-tracing experiments were performed in adult mice. The Lgr5-positive crypt base columnar cell generated all epithelial lineages over a 60-day period, suggesting that it represents the stem cell of the small intestine and colon. The expression pattern of Lgr5 suggests that it marks stem cells in multiple adult tissues and cancers.

The self-renewing epithelium of the small intestine is ordered into stem/progenitor crypt compartments and differentiated villus compartments. Recent evidence indicates that the Wnt cascade is the dominant force in controlling cell fate along the crypt-villus axis. Here we show a rapid, massive conversion of proliferative crypt cells into post-mitotic goblet cells after conditional removal of the common Notch pathway transcription factor CSL/RBP-J. We obtained a similar phenotype by blocking the Notch cascade with a gamma-secretase inhibitor. The inhibitor also induced goblet cell differentiation in adenomas in mice carrying a mutation of the Apc tumour suppressor gene. Thus, maintenance of undifferentiated, proliferative cells in crypts and adenomas requires the concerted activation of the Notch and Wnt cascades. Our data indicate that gamma-secretase inhibitors, developed for Alzheimer's disease, might be of therapeutic benefit in colorectal neoplastic disease.

In a phenotypic screen in mice using a gene trap approach in embryonic stem cells, we have identified a recessive loss-of-function mutation in the mgcRacGAP gene. Maternal protein is present in the oocyte, and mgcRacGAP gene transcription starts at the four-cell stage and persists throughout mouse pre-implantation development. Total mgcRacGAP deficiency results in pre-implantation lethality. Such E3.5 embryos display a dramatic reduction in cell number, but undergo compaction and form a blastocoel. At E3.0-3.5, binucleated blastomeres in which the nuclei are partially interconnected are frequently observed, suggesting that mgcRacGAP is required for normal mitosis and cytokinesis in the pre-implantation embryo. All homozygous mutant blastocysts fail to grow out on fibronectin-coated substrates, but a fraction of them can still induce decidual swelling in vivo. The mgcRacGAP mRNA expression pattern in post-implantation embryos and adult mouse brain suggests a role in neuronal cells. Our results indicate that mgcRacGAP is essential for the earliest stages of mouse embryogenesis, and add evidence that CYK-4-like proteins also play a role in microtubule-dependent steps in the cytokinesis of vertebrate cells. In addition, the severe phenotype of null embryos indicates that mgcRacGAP is functionally non-redundant and cannot be substituted by other GAPs during early cleavage of the mammalian embryo. ispartof: Mechanisms of Development vol:102 issue:1 pages:33-44 ispartof: location:Ireland status: published

SummarySmall 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.