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Small cell lung cancer (SCLC) is an aggressive malignancy characterized by early metastasis and extreme lethality. The backbone of SCLC treatment over the past several decades has been platinum-based doublet chemotherapy, with the recent addition of immunotherapy providing modest benefits in a subset of patients. However, nearly all patients treated with systemic therapy quickly develop resistant disease, and there is an absence of effective therapies for recurrent and progressive disease. Here we conducted CRISPR-Cas9 screens using a druggable genome library in multiple SCLC cell lines representing distinct molecular subtypes. This screen nominated exportin-1, encoded by XPO1, as a therapeutic target. XPO1 was highly and ubiquitously expressed in SCLC relative to other lung cancer histologies and other tumor types. XPO1 knockout enhanced chemosensitivity, and exportin-1 inhibition demonstrated synergy with both first- and second-line chemotherapy. The small molecule exportin-1 inhibitor selinexor in combination with cisplatin or irinotecan dramatically inhibited tumor growth in chemonaïve and chemorelapsed SCLC patient-derived xenografts, respectively. Together these data identify exportin-1 as a promising therapeutic target in SCLC, with the potential to markedly augment the efficacy of cytotoxic agents commonly used in treating this disease. Significance: CRISPR-Cas9 screening nominates exportin-1 as a therapeutic target in SCLC, and exportin-1 inhibition enhances chemotherapy efficacy in patient-derived xenografts, providing a novel therapeutic opportunity in this disease.

The eventual development of resistance to single-agent targeted therapies in lung adenocarcinomas (LUAD) is inevitable, and new strategies are needed. We hypothesize that combination therapies aimed at a known driver and a distinct targetable alteration could prolong time on oral targeted therapy. In an analysis of 7636 patients with LUAD who underwent MSK-IMPACT large panel NGS testing, 5.5% (416/7636) harbored MDM2 amplification (MDM2amp), a known mechanism of TP53 inactivation. MDM2amp was over-represented among tumors with alterations in METex14 (34.4%, p Citation Format: Arielle Elkrief, Vladimir Markov, Álvaro Quintanal-Villalonga, Rebecca Caeser, Pawel Sobczuk, Emily Cheng, Alexander Drilon, Gregory J. Riely, William W. Lockwood, Elisa de Stanchina, Charles M. Rudin, Igor Odintsov, Romel Somwar. MDM2 inhibition in combination with MEK inhibition in pre-clinical models of lung adenocarcinomas with MDM2 amplification [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 6127.

The impact of the intratumoral microbiome on immune checkpoint inhibitor (ICI) efficacy in patients (pts) with non-small cell lung cancer (NSCLC) is unknown. In preclinical studies, the presence of lung intratumoral Escherichia was associated with a proinflammatory tumor microenvironment and decreased metastases within lung tissue. We sought to detect intratumoral bacteria in pts with advanced NSCLC using hybrid capture-based, next generation sequencing (NGS). We studied 849 pts treated with ICI-based therapy who underwent NGS at our center. We extracted unmapped reads from BAM files, and these were queried for bacteria (blastn alignment using the NCBI database). Putative environmental contaminants were subtracted from the analysis using “no template” controls (n=2,539) to exclude possible artifactual false positives. A custom E.Coli fluorescence in situ hybridization (FISH) probe was used to visualize Escherichia within the tumors after co-registration with H&E. In 849 pts, a median of 30 bacterial reads was detected per sample (inter-quartile range (18-85)). Among 68 pts with paired primary/metastatic samples, the bacterial spectra were similar in both sites, suggesting that tumor resident bacteria might travel with cancer cells to distant sites. Antibiotic use within 30 days of tumor sampling was associated with decreased intratumoral bacterial diversity (p=0.023 by Inverse Simpson, p=0.038 by Shannon). Intratumoral Escherichia was associated with better PFS (HR 0.78, 95% CI 0.62-0.98, p=0.036), and OS (HR 0.74, 95% CI 0.58-0.95, p=0.017) in pts treated with single-agent ICI, but not combination Chemo/ICI. In a multivariable model adjusting for prognostic features in NSCLC including PD-L1 tumor proportion score, the presence of intratumoral Escherichia was associated with better PFS (p=0.040) and OS (p=0.045) upon single-agent ICI therapy. Escherichia appeared to be intracellular based on co-registration of FISH staining and serial H&E sections. These findings warrant further investigation of the possible inter-relationships between intratumoral Escherichia, tumor immune micro-environment, and ICI therapeutic outcomes. Citation Format: Arielle Elkrief, Anita S. Bowman, Ayyuce Begum Bektas, Wenfei Kang, Katia Manova-Todorova, Jacklynn V. Egger, Hira Rizvi, Daniel Kelly, Eric Chan, Eric Rosiek, Fan Ning, Gregory J. Riely, Álvaro Quintanal Villalonga, Snjezana Dogan, Umesh Bhanot, Mithat Gonen, Matthew D. Hellmann, Adam J. Schoenfeld, Charles M. Rudin, Marc Ladanyi, Chad M. Vanderbilt. Intratumoral Escherichia is associated with response to single-agent immune checkpoint inhibition in patients with advanced non-small 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 5185.

Lung adenocarcinoma (LUAD), constituting 50% of non-small cell lung cancer, is classically defined by the presence of driver mutations in oncogenes such as KRAS, EGFR, and BRAF. While the development of driver-targeted therapies has significantly improved survival in subsets of patients with LUAD, studies examining tumor sequencing data and clinical outcomes have shown that intra-driver genetic and phenotypic heterogeneity underlie differential patient responses to these therapies. In particular, co-occurring alterations in the genes SMARCA4 (BRG1), STK11 (LKB1), and KEAP1 are predictive of exceptionally poor prognosis and worse overall survival in metastatic LUAD patients. SMARCA4 loss is also a hallmark of undifferentiated, highly chemoresistant NSCLC tumors. While these co-mutations most often appear in KRAS-driven tumors, their association with poor outcomes is maintained regardless of driver status. Studies exploring the molecular features of SMARCA4-deficient and STK11/KEAP1 co-mutant LUAD have yielded translational insights specific to these subsets, establishing a rationale to characterize the unique biology of SMARCA4/STK11/KEAP1 (BLK) triple-mutant LUAD. To this end, we are profiling BLK LUAD through a combination of genomic, transcriptomic, epigenomic, and phenotypic assays in in vitro models. We have generated paired isogenic in vitro models of BLK LUAD via CRISPR-Cas9 knockout. Phenotypic analyses of these cell lines, whose engineered genotypes model varying combinations of SMARCA4, KEAP1, and STK11 loss, have revealed growth rate differences in vitro, and pairwise comparisons of RNA-sequencing in these lines show downregulation of lung differentiation markers and upregulation of metastasis-associated genes concomitant with SMARCA4 loss. In conclusion, we have generated isogenic preclinical models showing molecular and phenotypic features consistent with observations reported in BLK LUADs. Further molecular and functional characterization of these models may reveal mechanistic insights into the biology of this subset of aggressive tumors. Citation Format: Emily Costa, Corrin Wohlheiter, Samuel Tischfield, Alister Funnell, JT Poirier, Álvaro Quintanal Villalonga, Triparna Sen, Charles Rudin. Characterizing SMARCA4/STK11/KEAP1 co-mutant lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 859.

Fibroblast growth factor receptor (FGFR)1 has been associated with tumorigenesis in a variety of tumors, including lung cancer. FGFR1 amplification is detected in up to 20% of lung squamous cell carcinomas, and was initially related to tumorigenesis and to response to FGFR inhibitors in preclinical models of this pathology. These data encouraged the establishment of FGFR1 amplification as the main eligibility criterion for inclusion of patients in FGFR inhibitors clinical trials. However, the use of FGFR inhibitors in FGFR1-amplified tumors has shown limited success, with only 5-10% of selected patients showing partial response, suggesting that this genomic aberration may not be a good predictive biomarker for the efficacy of these inhibitors. In this work, we provide in vitro and in vivo data showing that the oncogenic effects of FGFR1 expression depend on the expression of the adhesion molecule N-cadherin in non-small cell lung cancer (NSCLC). In line with these results, FGFR1 expression correlates with poorer prognosis only in tumors with high N-cadherin levels in two independent NSCLC patient cohorts. We observed that high FGFR1 expression alone is not sufficient to predict FGFR inhibition efficacy in lung cancer cell lines and patient-derived xenografts, with only high FGFR1- and high N-cadherin-expressing models responding to selective FGFR inhibitors. Altogether, our data show that the determination of the expression of FGFR1 alone is not sufficient to predict FGFR inhibition efficacy. The co-determination of N-cadherin expression may optimize patient selection for this therapeutic strategy. Citation Format: Álvaro Quintanal-Villalonga, Irene Ferrer, Ángela Marrugal, Laura Ojeda-Márquez, Jon Zugazagoita, Laura García-Redondo, Fernando López-Ríos, Luis Montuenga, Sonia Molina-Pinelo, Sonia Molina-Pinelo, Amancio Carnero, Luis Paz-Ares. Novel predictor of FGFR1 inhibition efficacy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2589.

The FGFR4-388Arg allele, where an arginine substitutes a glycine in the 388 codon of the FGFR4 gene, has been associated to poorer patient outcome in different tumor types. In lung cancer, the variant has been related to shorter overall survival in adenocarcinoma (ADC) patients, while no relationship with squamous cell carcinoma prognosis (SCC) has been reported. Mechanistically, the FGFR4-388Arg variant has been related to increased MAPK pathway activation and to EMT in prostate cancer in vitro models. Furthermore, the variant has been associated with higher STAT3 signaling in murine models of breast and lung cancer. However, so far the molecular biology for this FGFR4 variant in lung cancer patients has not been addressed. We overexpressed the FGFR4-388Gly and FGFR4-388Arg variants in lung cancer cell lines from different histologic backgrounds and performed tumorogenicity surrogate assays and downstream signaling activation assessment. In the generated stable cell lines, we also determined the expression of EMT markers. Furthermore, we determined the FGFR4 variant and the FGFR4 and N-cadherin mRNA expression in a cohort of NSCLC patients (N=65) and correlated these data to patient outcome. We reported that FGFR4-388Arg increases tumorogenicity in lung cancer cell lines. Mechanistically, these functional effects seem to be mediated by MAPK and STAT3 overactivation and by the induction of an EMT phenotype, which includes N-cadherin increased expression. In fact, this induction of N-cadherin protein expression by the FGFR4-388Arg variant seems to be responsible for the pro-oncogenic effects reported. In NSCLC patient tumor samples, the FGFR4-388Arg variant correlates with higher N-cadherin expression and with poorer survival. In conclusion, the FGFR4-388Arg variant is a potential prognostic biomarker in NSCLC, including ADC and SCC patients. This variant increases tumorogenesis through the activation of MAPK and STAT3 signaling pathways and through the promotion of an EMT phenotype. Citation Format: Álvaro Quintanal-Villalonga, Rocío Suárez, Laura Ojeda-Márquez, Santiago Ponce-Aix, Amancio Carnero, Luis Paz-Ares, Irene Ferrer, Sonia Molina-Pinelo. The FGFR4-388Arg variant exerts pro-tumorogenic effects in lung cancer by inducing an EMT phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3334. doi:10.1158/1538-7445.AM2017-3334

FGFR family of proteins has been extensively related to oncogenic properties in several types of tumors, including lung cancer. Among its members, FGFR1 has been related to squamous cell lung carcinoma, where FGFR1 amplification is present in 20% of patients. However, its role in lung cancer has not yet been thoroughly described. Several lung cancer cell lines with different genetic backgrounds were transfected with plasmids to either overexpress or silence FGFR1. Then several tumorigenic abilities were tested in vitro and in vivo. mRNA from Paraffin-embedded tissue of a cohort of lung cancer patients was extracted and FGFR1 expression levels were measured and related to clinical characteristics. FGFR1 increases oncogenic properties in SCC cell lines, but exerts anti-oncogenic effects in several lung ADC cell lines, suggesting a tumor suppressor role under certain circumstances. This is a consequence of differentially expressed genes among these two histologies. According to this, analysis of FGFR1 mRNA expression of a cohort of lung cancer patients revealed that high FGFR1 mRNA expression was associated to a shorter overall survival (OS) and progression free survival (PFS) in lung SCC patients. However, a trend for longer OS was observed for the ADC patients with higher FGFR1 mRNA expression. FGFR1 has the potential to be either a tumor suppressor or an oncogene and the molecular context is a determining factor to define its final role in tumorigenesis. Citation Format: Álvaro Quintanal-Villalonga, Laura Ojeda-Márquez, Ángela Marrugal, Rocío Suárez, Irene Ferrer, Amancio Carnero, Sonia Molina-Pinelo, Luis Paz-Ares. FGFR1 can act as an oncogene or a tumor suppressor depending on the molecular context. [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 1122.