Brief Report: Comprehensive Clinicogenomic Profiling of Small Cell Transformation From EGFR-Mutant NSCLC Informs Potential Therapeutic Targets

Introduction

NSCLC transformation to SCLC has been best characterized with EGFR-mutant NSCLC, with emerging case reports seen in ALK, RET, and KRAS-altered NSCLC. Previous reports revealed transformed SCLC from EGFR-mutant NSCLC portends very poor prognosis and lack effective treatment. Genomic analyses revealed TP53 and RB1 loss of function increase the risk of SCLC transformation. Little has been reported on the detailed clinicogenomic characteristics and potential therapeutic targets for this patient population.

Methods

In this study, we conducted a single-center retrospective analysis of clinical and genomic characteristics of patients with EGFR-mutant NSCLC transformed to SCLC. Demographic data, treatment course, and clinical molecular testing reports were extracted from electronic medical records. Kaplan-Meier analyses were used to estimate survival outcomes. Next generation sequencing-based assays was used to identify EGFR and co-occurring genetic alterations in tissue or plasma before and after SCLC transformation. Single-cell RNA sequencing (scRNA-seq) was performed on a patient-derived-xenograft model generated from a patient with EGFR-NSCLC transformed SCLC tumor.

Results

A total of 34 patients were identified in our study. Median age at initial diagnosis was 58, and median time to SCLC transformation was 24.2 months. 68% were female and 82% were never smokers. 79% of patients were diagnosed as stage IV disease, and over half had brain metastases at baseline. Median overall survival of the entire cohort was 38.3 months from initial diagnoses and 12.4 months from time of SCLC transformation. Most patients harbored EGFR exon19 deletions as opposed to exon21 L858R alteration. Continuing EGFR tyrosine kinase inhibitor post-transformation did not improve overall survival compared with those patients where tyrosine kinase inhibitor was stopped in our cohort. In the 20 paired pretransformed and post-transformed patient samples, statistically significant enrichment was seen with PIK3CA alterations (p = 0.04) post-transformation. Profiling of longitudinal liquid biopsy samples suggest emergence of SCLC genetic alterations before biopsy-proven SCLC, as shown by increasing variant allele frequency of TP53, RB1, PIK3CA alterations. ScRNA-seq revealed potential therapeutic targets including DLL3, CD276 (B7-H3) and PTK7 were widely expressed in transformed SCLC.

Conclusions

SCLC transformation is a potential treatment resistance mechanism in driver-mutant NSCLC. In our cohort of 34 EGFR-mutant NSCLC, poor prognosis was observed after SCLC transformation. Clinicogenomic analyses of paired and longitudinal samples identified genomic alterations emerging post-transformation and scRNA-seq reveal potential therapeutic targets in this population. Further studies are needed to rigorously validate biomarkers and therapeutic targets for this patient population.

Targeting BCL2 Overcomes Resistance and Augments Response to Aurora Kinase B Inhibition by AZD2811 in Small Cell Lung Cancer

PURPOSE

Therapeutic resistance to frontline therapy develops rapidly in small cell lung cancer (SCLC). Treatment options are also limited by the lack of targetable driver mutations. Therefore, there is an unmet need for developing better therapeutic strategies and biomarkers of response. Aurora kinase B (AURKB) inhibition exploits an inherent genomic vulnerability in SCLC and is a promising therapeutic approach. Here, we identify biomarkers of response and develop rational combinations with AURKB inhibition to improve treatment efficacy.

EXPERIMENTAL DESIGN

Selective AURKB inhibitor AZD2811 was profiled in a large panel of SCLC cell lines (n = 57) and patient-derived xenograft (PDX) models. Proteomic and transcriptomic profiles were analyzed to identify candidate biomarkers of response and resistance. Effects on polyploidy, DNA damage, and apoptosis were measured by flow cytometry and Western blotting. Rational drug combinations were validated in SCLC cell lines and PDX models.

RESULTS

AZD2811 showed potent growth inhibitory activity in a subset of SCLC, often characterized by, but not limited to, high cMYC expression. Importantly, high BCL2 expression predicted resistance to AURKB inhibitor response in SCLC, independent of cMYC status. AZD2811-induced DNA damage and apoptosis were suppressed by high BCL2 levels, while combining AZD2811 with a BCL2 inhibitor significantly sensitized resistant models. In vivo, sustained tumor growth reduction and regression was achieved even with intermittent dosing of AZD2811 and venetoclax, an FDA-approved BCL2 inhibitor.

CONCLUSIONS

BCL2 inhibition overcomes intrinsic resistance and enhances sensitivity to AURKB inhibition in SCLC preclinical models.

Abstract 6206: Combined inhibition of AXL and ATR enhances replication stress, cell death and immune response in small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung tumor. Despite high initial responses to frontline chemo-immunotherapy, therapeutic resistance develops rapidly. There are limited treatment options in the relapsed setting, where the prognosis remains dismal. SCLC tumors experience continuous and high levels of replication stress (RS) due to ubiquitous loss of key cell cycle checkpoints, RB1 and TP53. Frequent amplification and high expression of the transcription factor cMYC further contribute to increased RS. Thus, high levels of RS expose a potential SCLC vulnerability and provide a therapeutic opportunity. Our group and others have shown that AXL, a TAM family receptor tyrosine kinase that is highly expressed in mesenchymal tumors, mediates resistance to chemotherapy, radiation and targeted therapies in SCLC, non-small cell lung cancer and other cancers, through its role in driving epithelial to mesenchymal transition (EMT). More recently, a novel role for AXL in DNA damage repair and tolerance has emerged. Therefore, we hypothesize that AXL targeting may be a potential therapeutic approach in SCLC. We first investigated the transcriptomic expression profile of AXL in SCLC clinical cohorts. AXL-high tumors were seen in a subset of treatment-naïve SCLC tumors, frequently among, but not limited to, the inflamed SCLC subtype. AXL expression was also seen in many relapsed SCLC tumors. As expected, tumors with high AXL expression also expressed several mesenchymal genes and higher EMT scores. Interestingly, among the treatment-naïve SCLC tumors, AXL expression was inversely correlated with a RS signature (rho=-0.54, p<0.001). Next, we tested the effects of AXL inhibition in SCLC in vitro and in vivo models. In a panel of 30 SCLC cell lines, bemcentinib, a selective AXL inhibitor in clinical trials for various advanced solid tumors, exhibited a range of antiproliferative activity, with IC50 values ranging from 41 nM to 10 µM (median IC50 3.1 µM). Bemcentinib also significantly delayed tumor growth in in vivo SCLC models. Biomarkers associated with sensitivity to bemcentinib in SCLC cell lines included markers of RS (cMYC, replication stress score) and DNA damage response (phospho CHK1S345, phospho CHK2T68). Bemcentinib also induced RS, indicated by the activation of ATR/CHK1-mediated RS response pathway, and DNA damage, and the combination with an ATR inhibitor (ceralasertib) showed a greater than additive effect. In a syngeneic model of SCLC, the combination of bemcentinib, ceralasertib and an anti-PDL1 antibody induced significant tumor regression. Together, these promising findings demonstrate that AXL inhibition may be an effective strategy to target the RS vulnerability common in SCLC.

Citation Format: Kavya Ramkumar, C. Allison Stewart, Azusa Tanimoto, Qi Wang, Yuanxin Xi, Benjamin B. Morris, Runsheng Wang, Li Shen, Robert J. Cardnell, Jing Wang, Carl M. Gay, Lauren A. Byers. Combined inhibition of AXL and ATR enhances replication stress, cell death and immune response in 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 6206.

Abstract 2602: Combined inhibition of AXL and ATR enhances cell death and immune response in small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive lung tumor of neuroendocrine origin with a dismal 5-year survival rate. Despite high response rates to initial therapy, rapid development of therapeutic resistance limits overall survival. There are also limited treatment options, particularly in the relapsed setting. Our group and others have shown that AXL, a TAM family receptor tyrosine kinase that is highly expressed in mesenchymal tumors, mediates resistance to chemotherapy, radiation and targeted therapies in SCLC, non-small cell lung cancer and other cancers, through its roles in driving epithelial to mesenchymal transition and DNA damage repair. AXL has also been implicated in immune escape. Based on these findings, we hypothesize that AXL targeting may be a potential therapeutic approach in SCLC. We screened BGB324 (bemcentinib), a selective small-molecule AXL inhibitor in clinical trials for various advanced solid tumors, in a panel of 60 human SCLC cell lines using cell viability assays. The SCLC cell lines showed a range of sensitivities, with IC50 values ranging from 41 nM to 10 µM (median IC50 3.1 µM) with NeuroD1-driven SCLC cell lines being highly sensitive to BGB324 (ANOVA p<0.05). BGB324 also showed potent inhibition of tumor growth in an in vivo SCLC model. BGB324 further combined synergistically with an ATR inhibitor (AZD3738) and induces significant DNA damage. In a syngeneic model of SCLC, the combination of BGB324, AZD6738 and an anti-PDL1 antibody combination also induced significant tumor regression. Together, these promising findings show that AXL inhibition may be effective in SCLC and support further investigation of AXL and ATR inhibitor combinations with immune checkpoint blockade.

Citation Format: Kavya Ramkumar, Azusa Tanimoto, C. Allison Stewart, Qi Wang, Li Shen, Robert J. Cardnell, B. Leticia Rodriguez, Don L. Gibbons, Jing Wang, Carl M. Gay, Lauren A. Byers. Combined inhibition of AXL and ATR enhances cell death and immune response in small cell lung cancer [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 2602.

SLFN11 biomarker status predicts response to lurbinectedin as a single agent and in combination with ATR inhibition in small cell lung cancer

Background

Lurbinectedin recently received FDA accelerated approval as a second line treatment option for metastatic small cell lung cancer (SCLC). However, there are currently no established biomarkers to predict SCLC sensitivity or resistance to lurbinectedin or preclinical studies to guide rational combinations.

Methods

Drug sensitivity was assayed in proliferation assays and xenograft models. Baseline proteomic profiling was performed by reverse-phase protein array. Lurbinectedin-induced changes in intracellular signaling pathways were assayed by Western blot.

Results

Among 21 human SCLC cell lines, cytotoxicity was observed following lurbinectedin treatment at a low dose (median IC50 0.46 nM, range, 0.06–1.83 nM). Notably, cell lines with high expression of Schlafen-11 (SLFN11) protein, a promising biomarker of response to other DNA damaging agents (e.g., chemotherapy, PARP inhibitors), were more sensitive to single-agent lurbinectedin (FC =3.2, P=0.005). SLFN11 was validated as a biomarker of sensitivity to lurbinectedin using siRNA knockdown and in xenografts representing SLFN11 high and low SCLC. Replication stress and DNA damage markers (e.g., γH2AX, phosphorylated CHK1, phosphorylated RPA32) increased in SCLC cell lines following treatment with lurbinectedin. Lurbinectedin also induced PD-L1 expression via cGAS-STING pathway activation. Finally, the combination of lurbinectedin with the ataxia telangiectasia and Rad3-related protein (ATR) inhibitors ceralasertib and berzosertib showed a greater than additive effect in SLFN11-low models.

Conclusions

Together our data confirm the activity of lurbinectedin across a large cohort of SCLC models and identify SLFN11 as a top candidate biomarker for lurbinectedin sensitivity. In SLFN11-low SCLC cell lines which are relatively resistance to lurbinectedin, the addition of an ATR inhibitor to lurbinectedin re-sensitized otherwise resistant cells, confirming previous observations that SLFN11 is a master regulator of DNA damage response independent of ATR, and the absence of SLFN11 leads to synthetic lethality with ATR inhibition. This study provides a rationale for lurbinectedin in combination with ATR inhibitors to overcome resistance in SCLC with low SLFN11 expression.

Abstract P079: The impact of BCL2 expression on sensitivity to the novel Aurora kinase B inhibitor AZD2811 in small cell lung cancer

Purpose: Small cell lung cancer (SCLC) is a highly lethal malignancy, with rapidly-acquired therapeutic resistance. In contrast to non-SCLC, treatment strategies based on molecular subtypes have not been well established. Aurora kinase family proteins (AURKA and AURKB) are essential for cell division, regulating chromosomal segregation during mitosis, and are upregulated in cancer. Our group has demonstrated that cMYC-driven SCLC tumors were susceptible to an AURKA inhibitor, alisertib, making AURK proteins an attractive targeted therapeutic approach. A novel AURKB inhibitor, AZD2811NP (nanoparticle), is now being investigated in relapsed SCLC patients (NCT02579226), but molecular mechanisms of resistance have not yet been identified. Here, we hypothesize that targeting predictive markers related to the effect of AZD2811 may reinforce susceptibility to AURKB inhibition. Experimental Design: We evaluated susceptibility to AZD2811 in 63 human-derived SCLC cell lines using 96-hour proliferation assays. To identify translatable biomarkers of response, we correlated AZD2811 IC50 values with genomic (whole exome sequencing, WES), transcriptomic (RNASeq), and proteomic profiling (Reverse Phase Protein Array, RPPA) data. We validated changes in apoptosis and DNA damage markers induced by AZD2811 in SCLC cells infected with the lentivirus vectors expressing BCL-2 and shRNA against BCL-2 using western blot. We used SCLC patient-derived xenograft (PDX) models with distinct BCL-2 profiles to evaluate in vivo antitumor effect. Results: In the SCLC cells treated with AZD2811, 15/63 (24%) and 10/63 (16%) cell lines showed high sensitivity (IC50<30 nM, Cmax) and intermediate sensitivity (IC50=30-100nM). Comparing protein expression, we found that cMYC (Fold change, FC:2.5; P = 0.015) were a positive biomarker of sensitivity, while high BCL-2 (FC:1.86; P = 0.032) associated with resistance. cMYC-high SCLC cell lines that were susceptible to AZD2811 became resistant when BCL-2 was overexpressed. Conversely, BCL-2 knock-down enhanced response to AZD2811, inducing apoptosis and DNA damage, in BCL-2-high cells that were originally resistant to single-agent AZD2811. Similar to Bcl-2 knock-down, treatment with venetoclax (a BCL-2 inhibitor routinely used in other cancers) enhanced apoptosis and DNA damage induction in combination with AZD2811 in cells overexpressing BCL-2. In PDX models with high BCL-2, combination of AZD2811 and venetoclax prominently induced tumor regression and apoptosis compared with each monotherapy, while there was no significant difference in PDX models with low BCL-2 between the combination and the monotherapy. Conclusions: Our preclinical results indicate that high BCL-2 expression reduced the efficacy of AZD2811 in SCLC models, but that Bcl2-driven resistance could be overcome with the combined use of BCL-2 and AURKB inhibitors. Findings support a promising rational combination therapy for BCL-2-high SCLC to enhance response to aurora kinase B inhibition.

Citation Format: Azusa Tanimoto, Carminia M. Della Corte, Kavya Ramkumar, Robert J. Cardnell, Allison C. Stewart, Carl M. Gay, Lauren Averett Byers, Qi Wang, Li Shen, Jing Wang, Jon Travers. The impact of BCL2 expression on sensitivity to the novel Aurora kinase B inhibitor AZD2811 in small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P079.

Lung Cancer Models Reveal Severe Acute Respiratory Syndrome Coronavirus 2-Induced Epithelial-to-Mesenchymal Transition Contributes to Coronavirus Disease 2019 Pathophysiology

INTRODUCTION

Coronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which enters host cells through the cell surface proteins ACE2 and TMPRSS2.

METHODS

Using a variety of normal and malignant models and tissues from the aerodigestive and respiratory tracts, we investigated the expression and regulation of ACE2 and TMPRSS2.

RESULTS

We find that ACE2 expression is restricted to a select population of epithelial cells. Notably, infection with SARS-CoV-2 in cancer cell lines, bronchial organoids, and patient nasal epithelium induces metabolic and transcriptional changes consistent with epithelial-to-mesenchymal transition (EMT), including up-regulation of ZEB1 and AXL, resulting in an increased EMT score. In addition, a transcriptional loss of genes associated with tight junction function occurs with SARS-CoV-2 infection. The SARS-CoV-2 receptor, ACE2, is repressed by EMT through the transforming growth factor-β, ZEB1 overexpression, and onset of EGFR tyrosine kinase inhibitor resistance. This suggests a novel model of SARS-CoV-2 pathogenesis in which infected cells shift toward an increasingly mesenchymal state, associated with a loss of tight junction components with acute respiratory distress syndrome-protective effects. AXL inhibition and ZEB1 reduction, as with bemcentinib, offer a potential strategy to reverse this effect.

CONCLUSIONS

These observations highlight the use of aerodigestive and, especially, lung cancer model systems in exploring the pathogenesis of SARS-CoV-2 and other respiratory viruses and offer important insights into the potential mechanisms underlying the morbidity and mortality of coronavirus disease 2019 in healthy patients and patients with cancer alike.

Targeting MYC-enhanced glycolysis for the treatment of small cell lung cancer

Introduction

The transcription factor MYC is overexpressed in 30% of small cell lung cancer (SCLC) tumors and is known to modulate the balance between two major pathways of metabolism: glycolysis and mitochondrial respiration. This duality of MYC underscores the importance of further investigation into its role in SCLC metabolism and could lead to insights into metabolic targeting approaches.

Methods

We investigated differences in metabolic pathways in transcriptional and metabolomics datasets based on cMYC expression in patient and cell line samples. Metabolic pathway utilization was evaluated by flow cytometry and Seahorse extracellular flux methodology. Glycolysis inhibition was evaluated in vitro and in vivo using PFK158, a small molecular inhibitor of PFKFB3.

Results

MYC-overexpressing SCLC patient samples and cell lines exhibited increased glycolysis gene expression directly mediated by MYC. Further, MYC-overexpressing cell lines displayed enhanced glycolysis consistent with the Warburg effect, while cell lines with low MYC expression appeared more reliant on oxidative metabolism. Inhibition of glycolysis with PFK158 preferentially attenuated glucose uptake, ATP production, and lactate in MYC-overexpressing cell lines. Treatment with PFK158 in xenografts delayed tumor growth and decreased glycolysis gene expression.

Conclusions

Our study highlights an in-depth characterization of SCLC metabolic programming and presents glycolysis as a targetable mechanism downstream of MYC that could offer therapeutic benefit in a subset of SCLC patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40170-021-00270-9.

Abstract 1022: Characterization of lurbinectedin as a single agent and in combinations with DNA damage response inhibitor for the treatment and bio-marker discovery of SCLC

Small-cell lung cancer (SCLC) is an aggressive neuroendocrine lung malignancy which is primarily driven by loss of function of tumor suppressor gene TP53 and RB1 and accounts for around 13-15% of all lung cancers. For metastatic SCLC the standard-of-care, first-line therapy is combination of platinum-based therapy with etoposide or with irinotecan. Though response rate in first-line chemotherapy in SCLC is very high, relapse is almost universal. For decades topotecan, a topoisomerase-I inhibitor was the only FDA approved second-line treatment in SCLC. However, on June 15th, 2020 the FDA approved lurbinectedin for treatment of patients with metastatic SCLC with disease progression from platinum-based chemotherapy and designated it as an orphan drug. Lurbinectedin (PM01183) is a synthetic analog of the natural marine-based tetrahydroisoquinoline, trabectedin which comes from the sea-squirt species Ecteinascidia turbinate. Lurbinectedin blocks transcription by inhibiting the activity of RNA-polymerase-II and inducing its specific degradation by the ubiquitin/proteasome machinery, also inducing DNA damage. Emerging data from our group, and others supports that SCLC is transcriptionally addicted via one of three main transcription factors ASCL1 (A), NeuroD1 (N) & POU2F3 (P), which may contribute to the promising results observed in SCLC trials to date with lurbinectedin. However, there are currently no established biomarkers to predict SCLC sensitivity or resistance to lurbinectedin. Furthermore, little is known regarding molecular changes in SCLC cells or other tumors upon exposure to lurbinectedin. In this preclinical study we investigated the therapeutic efficacy of lurbinectedin in large number of profiled SCLC cell lines representing the four SCLC subtypes (A, N, P and I) to identify candidate markers of drug sensitivity and resistance. In 12 human-derived and 3 mouse model-derived SCLC cell lines, the majority of cell lines were highly sensitive to lurbinectedin at a very low doses (median IC50 0.52 nM, range 0.08-1.84nM). We also observed increased markers of DNA damage following treatment in sensitive cell lines (e.g., γH2AX, ChK1, RPA32) by western blot. Notably, no subtype specific difference in lurbinectedin sensitivity was observed among the four subtypes (A, N, P and I) of SCLC cells. However, cell lines with higher SLFN11 expression were more sensitive to lurbinectedin. Western blot experiments showed significant increase in phosphorylation of γH2AX, ChK1, RPA32 in lurbinectedin treated SCLC cells compared to DMSO treatment. Together our preliminary data confirm lurbinectedin as a potent treatment option for SCLC, and support a rationale for potential combinations with other DNA damaging agents.

Citation Format: Kiran Kundu, Robert J. Cardnell, Li Shen, C. Allison Stewart, Kasey Cargill, Carl M. Gay, Jing Wang, Lauren A. Byers. Characterization of lurbinectedin as a single agent and in combinations with DNA damage response inhibitor for the treatment and bio-marker discovery of SCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1022.

Abstract 22: A novel, inflamed small cell lung cancer transcriptional subtype, SCLC-I, defines a subset of patients with distinct immunotherapy vulnerability

Background

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with dismal survival outcomes and no established predictive biomarkers. The landmark randomized, phase III IMpower133 trial established the new frontline standard of care for extensive-stage SCLC (ES-SCLC) as etoposide/platinum (EP) plus immune checkpoint blockade (ICB) [anti-PD-L1; atezolizumab (atezo)] based on an overall survival (OS) benefit compared to EP plus placebo. However, this survival benefit is limited in unselected populations, emphasizing the need for predictive biomarkers. Preclinically, there is emerging evidence of transcriptional heterogeneity among SCLC tumors, but the impact on therapeutic benefit remains undefined. Using non-negative matrix factorization (NMF) analysis of gene expression data from 81 SCLC tumors samples, we previously identified four subtypes, including three defined largely by differential expression of the transcription factors ASCL1 (SCLC-A), NEUROD1 (SCLC-N), and POU2F3 (SCLC-P), and a novel, fourth subtype with low expression of all three transcription factor signatures.

Method and Results

Using transcriptional and proteomic data from patient tumors and tumor-derived models, we molecularly characterized each of the four identified subtypes. The previously undescribed fourth subtype, dubbed SCLC-Inflamed (SCLC-I) showed high expression of non-neuroendocrine transcription factors (e.g. REST) and markers of EMT. Most distinctly, relative to the “cold” immune microenvironment typical of SCLC tumors, SCLC-I tumors possess markedly higher expression of interferon-γ signatures and immune checkpoints, including CD274 (PD-L1). Furthermore, cell type deconvolution using CIBERSORTx identified significantly higher infiltration into SCLC-I tumors by multiple immune cell types including T-cells, NK cells, macrophages, and dendritic cells. We predicted SCLC-I might derive disproportionate benefit from ICB due to its inflamed features. To test this, we applied our NMF-derived gene signature to 276 treatment-naïve, ES-SCLC patient tumors from the IMpower133 trial to assign patient subtype. The distribution of subtypes was as follows: SCLC-A 51%, SCLC-N 23%, SCLC-I 18% and SCLC-P 7%. While there was a trend toward OS benefit with the addition of atezo in each subtype, the benefit was numerically greater in SCLC-I. Specifically, median OS (atezo vs placebo arm) in months (mo) was 18.2 mo vs 10.4 mo for SCLC-I tumors, while median OS for the other three subtypes ranged from 9.6-10.9 mo (atezo arm) and 6.0-10.6 mo (placebo arm).

Conclusion

Unbiased transcriptional analyses identify four subtypes with distinct tumor and immune features. While all subtypes experienced improved OS with addition of anti-PD-L1 to frontline EP, SCLC-I patients appear to experience the most durable benefit.

Citation Format: Carl M. Gay, C. Allison Stewart, Lixia Diao, Barzin Y. Nabet, Junya Fujimoto, Luisa M. Solis, Wei Lu, Yuanxin Xi, Robert J. Cardnell, Natalie I. Vokes, Kavya Ramkumar, Stephen G. Swisher, Jack A. Roth, Bonnie S. Glisson, David S. Shames, Ignacio I. Wistuba, Jing Wang, John Minna, John V. Heymach, Lauren A. Byers. A novel, inflamed small cell lung cancer transcriptional subtype, SCLC-I, defines a subset of patients with distinct immunotherapy vulnerability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 22.

Abstract 2335: Targeting MYC-enhanced glycolysis in small cell lung cancer

Small cell lung cancer (SCLC) accounts for approximately 15% of lung cancer cases with a poor five year survival rate of 6%. The National Cancer Institute has designated SCLC as one of two “recalcitrant” cancers and urges translational research to advance treatment options. In our effort to maximize treatment benefits, we have aimed our investigation at uncovering metabolic differences contributing to disease progression that may be targeted through specific pathway inhibition. Although metabolism is relatively unstudied in SCLC, metabolic reprogramming is recognized as a hallmark of cancer and can be regulated by several different mechanisms. Notably, the transcription factor MYC is overexpressed in 30% SCLC tumors and is known to modulate the balance between two major pathways of metabolism: glycolysis and mitochondrial respiration. While mitochondrial respiration is the preferred source of energy production in terminally differentiated cells, many cancer cells switch to become predominantly glycolytic in an effort to generate energy quickly and produce biomolecules and electron carriers required for proliferation—a phenomena known as the Warburg Effect. Since MYC is expressed in only a subset of highly aggressive SCLC, we applied bimodal separation to both patient and cell line SCLC datasets to establish defined MYC subsets (MYCLow; MYCHigh) and performed gene ontology pathway analysis to genes that were significantly upregulated among the MYC-expressing samples. This revealed that 37% of significantly upregulated genes were linked to metabolic processes and further investigation showed many of those genes were linked to the glycolysis pathway. We also confirmed upregulation of protein expression through reverse phase protein array (RPPA). With glycolysis proving to be increased in MYCHigh samples, we simultaneously characterized pathway utilization in cell lines at baseline and in the presence of a potent glycolysis inhibitor. MYCHigh cell lines exhibited greater glucose consumption and lactate secretion, which was significantly decreased by glycolytic inhibition. Likewise, mitochondrial analysis revealed lower oxygen consumption and ATP production that were further reduced in the presence of the glycolysis inhibitor. Although mitochondrial density was unchanged regardless of MYC expression or glycolytic inhibition, reactive oxygen species (ROS) generation was greatly enhanced in the MYCHigh subset upon suppression of glycolysis. Lastly, SCLC xenografts derived from a MYCHigh SCLC cell line showed significantly slower tumor growth whereas MYCLow derived xenografts exhibited no significant difference in tumor growth. Together, these data provide evidence of metabolic differences among SCLC subsets such that MYC expression induces reliance on glycolysis, which can be targeted for therapeutic intervention.

Citation Format: Kasey R. Cargill, C. Allison Stewart, Elizabeth M. Park, Robert J. Cardnell, You Hong Fan, Qi Wang, Lixia Diao, Wai Kin Chan, Philip L. Lorenzi, Jing Wang, Lauren A. Byers. Targeting MYC-enhanced glycolysis in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2335.

Abstract 2758: Multiplex immunofluorescence (mIF) reveals differences in tumor immune microenvironment between molecularly-defined subsets of small cell lung cancer

Introduction: Despite the recent approval of immune checkpoints inhibitors (ICI) as a treatment option in the extensive-stage small cell lung cancer (SCLC) setting, survival has not significantly changed in the last decades. Recent scientific efforts have led to the identification of 4 major subtypes defined by expression of three transcription factors: ASCL1 (SCLC-A), NEUROD1 (SCLC-N), POU2F3 (SCLC-P) with the fourth subtype characterized by increased expression of immune genes (Inflamed subtype - SCLC-I). Transcriptomic results, along with recent immunotherapy trials, suggest that modulation of tumor immune microenvironment (TIME) could potential be critical to achieving clinical responses in a subset of patients, hence a comprehensive study of the TIME in SCLC is imperative. Here we report the feasibility of a multiplex immunofluorescence (mIF) methodology to analyze the TIME in SCLC.

Methods: FFPE sections from surgically resected SCLC (N=4, one representative case across all SCLC subtypes) were identified from the ICON Project at UT MD Anderson Cancer Center. We used mIF to identify and quantify immune markers grouped into two 6-antibody panels: Panel 1: cytokeratin (CK, AE1/AE3), CD3, CD8, PD-1, PD-L1 and CD68; Panel 2: CK, CD20, granzyme B, FOXP3, CD45RO, and CD57. Finally, genomic (WES), transcriptomic (RNA sequencing) and proteomic (RPPA) data from these cases were integrated with the mIF data.

Results: SCLC molecular subtypes (SCLC-A, N, P, I) were classified using transcriptomic and proteomic data. Analysis of TIME unveils a higher immune cell infiltration within SCLC-I subtype compared with the other cases representing, immune “cold” SCLC subtypes. SCLC-I subtype showed a 2-13 folder higher (range) immune cell density than SCLC-A, N and P subtypes (measured as a median of cell density). Specifically, T cells (CD3+) (695 and 242 cells/mm2, for SCLC-I and the median for the other subtypes respectively), T cytotoxic cells (CD3+ CD8+) (206 and 105), activated T cells (CD3+ CD8+ granzyme+) (20 and 2), antigen experienced ‘like' T cells (CD3+ PD-1+) (17 and 0), memory T cells (CD3+ CD45RO+) (328 and 91) and macrophages (CD68+) (773 and 57). PD-L1 expression in malignant cells did not show significant differences within the 4 SCLC subtypes. However, PD-L1 expression in macrophages was significantly higher in the SCLC-I subtype, suggesting an increase of IFN-gamma in the TIME.

Conclusions: TIME study show the use of mIF in SCLC tumors to be feasible, and could potentially provide key information towards the identification of SCLC patients that could benefit from ICI. For the first time we complemented transcriptomic data from SCLC tumors with mIF analysis unveiling the complex interplay of the host immune response and malignant cells. Our preliminary results warrant further studies to explore the role of TIME in immunotherapeutic response in SCLC.

Citation Format: Pedro Rocha, C. Allison Stewart, Edwin Parra, Luisa M. Solis, Carl M. Gay, Robert J. Cardnell, Naohiro Uraoka, Alejandro Francisco-Cruz, Hitoshi Dejima, Yuanxin Xi, Lixia Diao, Jing Wang, Marcelo V. Negrao, Jianjun Zhang, Ignacio Wistuba, Don L. Gibbons, Lauren A. Byers. Multiplex immunofluorescence (mIF) reveals differences in tumor immune microenvironment between molecularly-defined subsets of small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2758.

Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities

Despite molecular and clinical heterogeneity, small cell lung cancer (SCLC) is treated as a single entity with predictably poor results. Using tumor expression data and non-negative matrix factorization, we identify four SCLC subtypes defined largely by differential expression of transcription factors ASCL1, NEUROD1, and POU2F3 or low expression of all three transcription factor signatures accompanied by an Inflamed gene signature (SCLC-A, N, P, and I, respectively). SCLC-I experiences the greatest benefit from the addition of immunotherapy to chemotherapy, while the other subtypes each have distinct vulnerabilities, including to inhibitors of PARP, Aurora kinases, or BCL-2. Cisplatin treatment of SCLC-A patient-derived xenografts induces intratumoral shifts toward SCLC-I, supporting subtype switching as a mechanism of acquired platinum resistance. We propose that matching baseline tumor subtype to therapy, as well as manipulating subtype switching on therapy, may enhance depth and duration of response for SCLC patients.

AXL Inhibition Induces DNA Damage and Replication Stress in Non-Small Cell Lung Cancer Cells and Promotes Sensitivity to ATR Inhibitors

AXL, a TAM (TYRO3, AXL, and MERTK) family receptor tyrosine kinase, is increasingly being recognized as a key determinant of resistance to targeted therapies, as well as chemotherapy and radiation in non-small cell lung cancer (NSCLC) and other cancers. We further show here that high levels of AXL and epithelial-to-mesenchymal transition were frequently expressed in subsets of both treatment-naïve and treatment-relapsed NSCLC. Previously, we and others have demonstrated a role for AXL in mediating DNA damage response (DDR), as well as resistance to inhibition of WEE1, a replication stress response kinase. Here, we show that BGB324 (bemcentinib), a selective small-molecule AXL inhibitor, caused DNA damage and induced replication stress, indicated by ATR/CHK1 phosphorylation, more significantly in TP53-deficient NSCLC cell lines. Similar effects were also observed in large-cell neuroendocrine carcinoma (LCNEC) cell lines. High AXL protein levels were also associated with resistance to ATR inhibition. Combined inhibition of AXL and ATR significantly decreased cell proliferation of NSCLC and LCNEC cell lines. Mechanistically, combined inhibition of AXL and ATR significantly increased RPA32 hyperphosphorylation and DNA double-strand breaks and induced markers of mitotic catastrophe. Notably, NSCLC cell lines with low levels of SLFN11, a known predictive biomarker for platinum and PARP inhibitor sensitivity, were more sensitive to AXL/ATR cotargeting. These findings demonstrate a novel and unexpected role for AXL in replication stress tolerance, with potential therapeutic implications. IMPLICATIONS: These findings demonstrate that the combination of AXL and ATR inhibitors could be a promising therapeutic combination for NSCLC, LCNEC, and other cancers.

Dual Inhibition of MEK and AXL Targets Tumor Cell Heterogeneity and Prevents Resistant Outgrowth Mediated by the Epithelial-to-Mesenchymal Transition in NSCLC

The epithelial-to-mesenchymal transition (EMT) is a dynamic epigenetic reprogramming event that occurs in a subset of tumor cells and is an initiating step toward invasion and distant metastasis. The process is reversible and gives plasticity to cancer cells to survive under variable conditions, with the acquisition of cancer stem cell-like characteristics and features such as drug resistance. Therefore, understanding survival dependencies of cells along the phenotypic spectrum of EMT will provide better strategies to target the spatial and temporal heterogeneity of tumors and prevent their ability to bypass single-inhibitor treatment strategies. To address this, we integrated the data from a selective drug screen in epithelial and mesenchymal KRAS/p53 (KP)-mutant lung tumor cells with separate datasets including reverse-phase protein array and an in vivo shRNA dropout screen. These orthogonal approaches identified AXL and MEK as potential mesenchymal and epithelial cell survival dependencies, respectively. To capture the dynamicity of EMT, incorporation of a dual fluorescence EMT sensor system into murine KP lung cancer models enabled real-time analysis of the epigenetic state of tumor cells and assessment of the efficacy of single agent or combination treatment with AXL and MEK inhibitors. Both two- and three-dimensional culture systems and in vivo models revealed that this combination treatment strategy of MEK plus AXL inhibition synergistically killed lung cancer cells by specifically targeting each phenotypic subpopulation. In conclusion, these results indicate that cotargeting the specific vulnerabilities of EMT subpopulations can prevent EMT-mediated drug resistance, effectively controlling tumor cell growth and metastasis. SIGNIFICANCE: This study shows that a novel combination of MEK and AXL inhibitors effectively bypasses EMT-mediated drug resistance in KRAS/p53-mutant non-small cell lung cancer by targeting EMT subpopulations, thereby preventing tumor cell survival.

Lung cancer models reveal SARS-CoV-2-induced EMT contributes to COVID-19 pathophysiology

COVID-19 is an infectious disease caused by SARS-CoV-2, which enters host cells via the cell surface proteins ACE2 and TMPRSS2. Using a variety of normal and malignant models and tissues from the aerodigestive and respiratory tracts, we investigated the expression and regulation of ACE2 and TMPRSS2. We find that ACE2 expression is restricted to a select population of highly epithelial cells. Notably, infection with SARS-CoV-2 in cancer cell lines, bronchial organoids, and patient nasal epithelium, induces metabolic and transcriptional changes consistent with epithelial to mesenchymal transition (EMT), including upregulation of ZEB1 and AXL, resulting in an increased EMT score. Additionally, a transcriptional loss of genes associated with tight junction function occurs with SARS-CoV-2 infection. The SARS-CoV-2 receptor, ACE2, is repressed by EMT via TGFbeta, ZEB1 overexpression and onset of EGFR TKI inhibitor resistance. This suggests a novel model of SARS-CoV-2 pathogenesis in which infected cells shift toward an increasingly mesenchymal state, associated with a loss of tight junction components with acute respiratory distress syndrome-protective effects. AXL-inhibition and ZEB1-reduction, as with bemcentinib, offers a potential strategy to reverse this effect. These observations highlight the utility of aerodigestive and, especially, lung cancer model systems in exploring the pathogenesis of SARS-CoV-2 and other respiratory viruses, and offer important insights into the potential mechanisms underlying the morbidity and mortality of COVID-19 in healthy patients and cancer patients alike.

Abstract 232: Comprehensive metabolic profiling and vulnerabilities to metabolic inhibitors among small cell lung cancer subtypes

Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor that constitutes approximately 14% of all lung cancers diagnosed in the United States. Despite recent advances in treatment options, recurrence is a major challenge and long-term survival remains poor underscoring the importance of investigating mechanisms of treatment resistance and therapeutic strategies. Interestingly, our laboratory has recently uncovered evidence for the classification of SCLC into distinct subtypes, each with unique gene expression patterns and therapeutic vulnerabilities. These subtypes are characterized by differential expression of the transcription factors ASCL1, NEUROD1, or POU2F3. A fourth subtype is negative for all three transcription factors and has prominent expression of immune genes, thus is termed the Inflamed subtype. These subtypes are associated with differences in drug sensitivity, biomarker signatures, and mechanisms of cellular growth. One facet of tumor biology that has not been explored across the subtypes, or in SCLC in general, is the metabolic mechanisms of energy generation. Although metabolic reprogramming from mitochondrial respiration to glycolysis is considered a major hallmark of cancer, increasing evidence suggests that mitochondrial or amino acid dependencies may also contribute to treatment resistance. Therefore, understanding the metabolic demand, particularly among the subtypes, is critical for the development of new therapies. To address this, gene set enrichment analysis was applied to 81 human SCLC tumors categorized by subtype, and revealed differential gene expression correlating to pathways such as fatty acid metabolism in POU2F3 and reactive oxygen species in Inflamed that was confirmed by reverse phase protein analysis (RPPA). Further, we evaluated nutrient requirements, glycolysis dependence, and mitochondrial function in human SCLC cell lines and found differences in glucose uptake and subsequent lactate generation between the subtypes suggesting that glycolysis inhibition may be effective in particular subsets. Based on this, we then tested the efficacy of PFK-158 (glycolysis inhibitor) on cellular proliferation and metabolic function in these cell lines, which revealed variations in susceptibility dependent on subtype classification. Together, this data serves to enhance the current understanding of SCLC mechanisms of growth and provides evidence for metabolic inhibition as a potential therapeutic opportunity.

Citation Format: Kasey R. Cargill, Carl M. Gay, Robert J. Cardnell, You-Hong Fan, Qi Wang, Lixia Diao, Jing Wang, Lauren A. Byers. Comprehensive metabolic profiling and vulnerabilities to metabolic inhibitors among small cell lung cancer subtypes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 232.

STING Pathway Expression Identifies NSCLC With an Immune-Responsive Phenotype

INTRODUCTION

Although the combination of anti-programmed cell death-1 or anti-programmed cell death ligand-1 (PD-L1) with platinum chemotherapy is a standard of care for NSCLC, clinical responses vary. Even though predictive biomarkers (which include PD-L1 expression, tumor mutational burden, and inflamed immune microenvironment) are validated for immunotherapy, their relevance to chemoimmunotherapy combinations is less clear. We have recently reported that activation of the stimulator of interferon genes (STING) innate immune pathway enhances immunotherapy response in SCLC. Here, we hypothesize that STING pathway activation may predict and underlie predictive correlates of antitumor immunity in NSCLC.

METHODS

We analyzed transcriptomic and proteomic profiles in two NSCLC cohorts from our institution (treatment-naive patients in the Profiling of Resistance Patterns and Oncogenic Signaling Pathways in Evaluation of Cancers of the Thorax study and relapsed patients in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination study) and The Cancer Genome Atlas (N = 1320). Tumors were stratified by STING activation on the basis of protein or mRNA expression of cyclic GMP-AMP synthase, phospho-STING, and STING-mediated chemokines (chemokine ligand 5 [CCL5] and C-X-C motif chemokine 10 [CXCL10]). STING activation in patient tumors and in platinum-treated preclinical NSCLC models was correlated with biomarkers of immunotherapy response.

RESULTS

STING activation is associated with higher levels of intrinsic DNA damage, targetable immune checkpoints, and chemokines in treatment-naive and relapsed lung adenocarcinoma. We observed that tumors with lower STING and immune gene expression show higher frequency of serine-threonine kinase 11 (STK11) mutations; however, we identified a subset of these tumors that are TP53 comutated and display high immune- and STING-related gene expression. Treatment with cisplatin increases STING pathway activation and PD-L1 expression in multiple NSCLC preclinical models, including adeno- and squamous cell carcinoma.

CONCLUSIONS

STING pathway activation in NSCLC predicts features of immunotherapy response and is enhanced by cisplatin treatment. This suggests a possible predictive biomarker and mechanism for improved response to chemoimmunotherapy combinations.

Abstract B15: The oral Chk1 inhibitor, SRA737, synergizes with immune checkpoint blockade in small-cell lung cancer (SCLC)

Background: Small-cell lung cancer (SCLC) is the most aggressive form of lung cancer. Despite the recent success of immunotherapy in other indications, only a minority of SCLC patients respond to immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) or programmed death ligand 1 (PD-L1) either as a monotherapy or combination. Therefore, there is a strong need to develop strategies to enhance the efficacy of immunotherapy in SCLC. Our group previously discovered that SCLC exhibits high expression of checkpoint kinase 1 (Chk1) and showed that preclinical in vivo models of SCLC respond to Chk1 inhibition. Based on data from others and our group, we hypothesized that targeting Chk1 can enhance antitumor immunity and synergize with ICB.

Results: SRA737 treatment decreased cell viability with a range of potencies in a panel of SCLC cell lines in vitro. This was accompanied by an induction of double-strand breaks in sensitive cell lines as demonstrated by increased γ-H2AX. Intriguingly, SRA737 also led to an increase in micronuclei formation and STING activation in cells in vitro. Cell surface and total PD-L1 protein were increased following SRA737 treatment in vitro, further supporting a potential benefit of combining the drug with immune checkpoint blockade therapy in vivo. As hypothesized, SRA737 showed strong synergy with anti-PD-L1 antibody in an immunocompetent xenograft SCLC model. Triple-knockout SCLC cells generated from a GEMM mouse model with conditional deletion of Trp53, Rb1 and p130 were implanted into the flank of B6129F1 mice. The mice were treated for three weeks with either IgG (control), SRA737 (100mg/kg, either 3/7 or 5/7 days), anti-PD-L1 (300ug, 1/7 days) or the combination. While anti-PD1 antibody treatment was largely ineffective, SRA737 significantly delayed tumor growth (at Day 21: T/C=0.30 for 3/7 days and T/C=0.28 for 5/7 days). Combination treatment with SRA737 and anti-PD-L1 demonstrated remarkable antitumor efficacy, resulting in stable disease following SRA737 schedule of 3/7 days (T/C=0.12) and tumor regressions following SRA737 schedule of 5/7 days (T/C=0.1). These effects were sustained after treatment cessation and the long-term survival benefit is being assessed.

Discussion: The intrinsic antitumor activity of the Chk1 inhibitor, SRA737, was significantly enhanced by addition of an anti-PD-L1 antibody, leading to tumor regressions in an immunocompetent SCLC model. Preliminary evidence suggests SRA737 induces micronuclei formation, STING activation and PD-L1 expression in tumor cells. Further studies to elucidate the mechanism of Chk1 inhibition-induced antitumor immunity in SCLC are ongoing. SRA737 is currently being tested in clinical trials both as a monotherapy and in combination with other agents. Given that the anti-PD-L1 antibody opdivo is now approved for SCLC, our data suggest intriguing possibilities for therapeutic synergy between the oral Chk1 inhibitor, SRA737, and ICB therapy that warrant further clinical investigation.

Citation Format: Triparna Sen, Snezana Milutinovic, Robert J. Cardnell, Lixia Diao, Youhong Fan, Ryan J. Hansen, Bryan Strouse, Michael P. Hedrick, Christian Hassig, Jing Wang, Lauren A. Byers. The oral Chk1 inhibitor, SRA737, synergizes with immune checkpoint blockade in small-cell lung cancer (SCLC) [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B15.

Abstract B064: The Aurora kinase A-inhibitor, alisertib, is a potential candidate for combination with immunotherapy in small cell lung cancer

Background: Small cell lung cancer (SCLC) is characterized by a loss of TP53 and RB1 and by amplification of MYC in about 25% of patients. Our group and others have shown that MYC-driven SCLC cell lines are vulnerable to Aurora Kinase A (AURKA) inhibition. Alisertib, a selective AURKA inhibitor, has also shown clinical efficacy in MYC-positive relapsed SCLC patients in combination with paclitaxel in a phase II trial (NCT02038647). AURKA regulates DNA chromosome alignment during cell division and thus its inhibition results in mitotic stress and subsequently DNA damage. We have previously demonstrated that DNA damage response (DDR) inhibitors synergize with immune checkpoint inhibition in SCLC in vivo models by activating a STING-mediated innate immune response. Based on these findings, we hypothesized that AURKA inhibition may activate the STING pathway and induce PD-L1 expression in SCLC. Methods: We compared AURKA gene expression among a panel of SCLC and NSCLC cell lines and, similarly, in tumor versus normal tissue in SCLC clinical dataset (Sato et al.). In parallel, we explored the landscape of STING and immune genes expression in two SCLC clinical datasets (George et al. and Sato et al.).We tested human and GEMM-derived SCLC cell lines for changes in immune and DDR-related protein expression by Western blot analysis after treatment with the AURKA-i alisertib. Results: AURKA gene expression was higher in SCLC cell lines as compared to NSCLC cell lines (p=0.023) and in SCLC tumors compared to normal tissue (FC=1.6; p<0.001), thus making AURKA an attractive target in SCLC. Furthermore, in SCLC clinical datasets, we found that CXCL10 and CCL5, the two downstream chemokines of STING pathway, are highly expressed in about 30% SCLC tumors and their expression is significantly associated with CMYC (Spearman Rho>0.45, p<0.001), possibly due to high baseline levels of replication stress and also to CD274, CD8 and other markers and chemokines suggestive of an inflamed immune microenvironment. We observed that in vitro treatment with alisertib (1µM for 72 hours) further increases the level of phospho-H2AX protein, a marker of DNA damage, along with PD-L1. Furthermore, alisertib treatment resulted in STING pathway activation, as indicated by increased phospho-STING_S366 and phospho-TBK1_S172 protein levels, in both human and murine SCLC cells. Conclusions: Our results demonstrate the potential of alisertib, the selective AURKA inhibitor, in modulation of PD-L1 and STING pathway activation in SCLC cells, thus supporting the rationale for in vivo testing with immunotherapy drugs. In particular, evaluation of this strategy in MYC-positive SCLC models could open new therapeutic investigations in this highly resistant SCLC subgroup.

Citation Format: Carminia M. Della Corte, Liz Lauren Ajpacaja, Robert J Cardnell, Carl M Gay, Lixia Diao, Qi Wang, Kavya Ramkumar, Allison C. Stewart, Rebecca B. Kow, Hannah E Stumpf, You-Hong Fan, Jing Wang, John V Heymach, Lauren A. Byers. The Aurora kinase A-inhibitor, alisertib, is a potential candidate for combination with immunotherapy in small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B064. doi:10.1158/1535-7163.TARG-19-B064

Abstract B024: Clinical, genomic, and immune landscape of the receptor tyrosine kinase AXL in non-small cell lung cancer

Therapeutic resistance limits effective treatment of non-small cell lung cancer (NSCLC) and a better understanding of mechanisms contributing to resistance and strategies to overcome these are urgently needed. AXL, a TAM family receptor tyrosine kinase, has emerged as a key determinant of resistance to chemotherapy, radiation and targeted therapies in NSCLC and other cancers, through its roles in mediating epithelial-mesenchymal transition (EMT) and immune escape. As several small-molecule AXL inhibitors and anti-AXL biologics are currently in clinical testing, AXL has emerged as a target of interest in treatment-resistant NSCLC. Here, we investigated AXL expression in NSCLC by analyzing genomic, transcriptomic and proteomic profiles across 3 treatment-naïve (1095 tumors) and 2 previously treated (245 tumors) clinical cohorts of lung adenocarcinoma and squamous cell carcinoma. While AXL expression did not vary with disease stage, tumor samples from patients with prior systemic treatment (and subsequent relapse) had significantly higher AXL expression and were more likely to have undergone EMT (based on our published EMT score), as compared to treatment-naïve NSCLC patients (p<0.001). Although AXL-high tumors were seen in all histologic subtypes, AXL levels were 1.4-fold higher in lung adenocarcinoma than in squamous cell carcinoma (p<0.001). Further analysis of driver genes in adenocarcinoma revealed that treatment-naïve NSCLC tumors with ALK translocations frequently had high expression of AXL at baseline (p=0.07), while approximately half of EGFR mutant NSCLC expressed high AXL mRNA. In contrast, tumors bearing mutations in STK11 and KEAP1 had relatively lower AXL expression (1.8-fold and 1.6-fold respectively, both p<0.001). Similarly, the KRAS/STK11 co-mutation subgroup, which is associated with higher rates of inactivating KEAP1 mutations and an immune suppressed phenotype, had lower AXL levels as compared to the KRAS/TP53 or KRAS/CDKN2A/B co-mutation subgroups (p<0.001). As AXL has been described to play a role in immune escape, we next investigated the association between AXL expression and immune response genes. AXL expression was strongly correlated with expression of immune suppressive mediators (TIM3, FOXP3, PD-L1 and PD-L2) as well as macrophage-recruiting factors (CCL2 and CSF-1). Furthermore, a significant correlation (rho > 0.3; p<0.001) between AXL expression and CXCL10 and CCL5, effector chemokines of STING-mediated innate immune response, was also observed in lung adenocarcinoma. In summary, our results show that AXL, which is associated with resistance to therapy, is present at higher levels in a significant subset of NSCLC tumors, including in treatment-naïve patients with ALK translocations and EGFR mutations. These findings suggest that early co-targeting of AXL along with standard therapies could improve therapeutic outcomes.

Citation Format: Kavya Ramkumar, Carminia M. Della Corte, Lixia Diao, Robert J. Cardnell, Vali A. Papadimitrakopoulou, John V. Heymach, Jing Wang, Don L. Gibbons, Lauren A. Byers. Clinical, genomic, and immune landscape of the receptor tyrosine kinase AXL in non-small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B024. doi:10.1158/1535-7163.TARG-19-B024

Combination Treatment of the Oral CHK1 Inhibitor, SRA737, and Low-Dose Gemcitabine Enhances the Effect of Programmed Death Ligand 1 Blockade by Modulating the Immune Microenvironment in SCLC

INTRODUCTION

Despite the enthusiasm surrounding cancer immunotherapy, most SCLC patients show very modest response to immune checkpoint inhibitor monotherapy treatment. Therefore, there is growing interest in combining immune checkpoint blockade with chemotherapy and other treatments to enhance immune checkpoint blockade efficacy. Based on favorable clinical trial results, chemotherapy and immunotherapy combinations have been recently approved by the U.S. Food and Drug Administration for frontline treatment for SCLC.

METHODS AND RESULTS

Here, we show that combined treatment of SRA737, an oral CHK1 inhibitor, and anti-programmed death ligand 1 (PD-L1) leads to an antitumor response in multiple cancer models, including SCLC. We further show that combining low, non-cytotoxic doses of gemcitabine with SRA737 + anti-PD-L1/anti-PD-1 significantly increased antitumorigenic CD8+ cytotoxic T cells, dendritic cells, and M1 macrophage populations in an SCLC model. This regimen also led to a significant decrease in immunosuppressive M2 macrophage and myeloid-derived suppressor cell populations, as well as an increase in the expression of the type I interferon beta 1 gene, IFNβ, and chemokines, CCL5 and CXCL10.

CONCLUSIONS

Given that anti-PD-L1/anti-PD-1 drugs have recently been approved as monotherapy and in combination with chemotherapy for the treatment of SCLC, and that the SRA737 + low dose gemcitabine regimen is currently in clinical trials for SCLC and other malignancies, our preclinical data provide a strong rational for combining this regimen with inhibitors of the PD-L1/PD-1 pathway.

Abstract 3772: Inter- and intra-tumoral variations in ASCL1, NEUROD1, and POU2F3 transcriptional programs underlie three distinct molecular subtypes of small cell lung cancers

Accounting for 15% of all lung cancer diagnoses, small cell lung cancer (SCLC) is an aggressive malignancy with dismal clinical outcomes, due in part to failure to define SCLC molecular subsets and identify the unique, targetable vulnerabilities therein. Recent data has begun to delineate these subsets by uncovering inter-tumoral heterogeneity in features such as DNA damage response, EMT, and neuroendocrine (NE) status. An integrated analysis of clinical samples to determine the implications of this heterogeneity broadly on SCLC classification has not yet been performed. Using RNAseq data from 81 SCLC tumor samples, we applied non-negative matrix factorization (NMF) which identified three clusters, each enriched for unique transcriptional programs driven by ASCL1 (30/81), NEUROD1 (24/81), or POU2F3 (27/81). These three genes encode transcription factors which define mutually exclusive NE-high, NE-low, and novel tuft cell variants of SCLC. Bulk RNAseq analyses of SCLC CTC-derived xenograft (CDX) models validated the clustering analysis in vivo. However, single-cell RNAseq from these same models reveals subtle evidence of intra-tumoral and intra-cellular heterogeneity in transcriptional programs that appear mutually exclusive in bulk analyses, suggesting plasticity among these variants. Guided by our NMF results, we performed RNAseq-based supervised clustering to classify each of 60 SCLC cell lines into ASCL1-driven, NEUROD1-driven, and POU2F3-driven clusters. Then, using reverse phase protein array data for these lines, we derived proteomic signatures for each cluster as follows: ASCL1-driven: E-cadherinhigh/TTF-1high/cMYClow, NEUROD1-driven: E-cadherinlow/TTF-1low/cMYChigh, and POU2F3-driven: E-cadherinhigh/TTF-1low/cMYChigh (ANOVA p<0.001 for each). Other targetable proteins vary significantly among these clusters including BCL-2 (lower in NEUROD1-driven; p<0.001) and PD-L1 (higher in ASCL1-driven; p=0.04). Correlating these clusters with IC50 values for over 500 drugs we find unique vulnerabilities. For example, POU2F3-driven lines were more sensitive to PARP inhibitors (PARPi), despite lacking biomarkers of PARPi sensitivity in SCLC (e.g. high SLFN11, low ATM). ASCL1-driven lines were more resistant to aurora kinase inhibitors (AURKi), as predicted given their lower expression of cMYC, a predictor of AURKi sensitivity in SCLC. Our data suggest that SCLC is subdivided on the basis of three unique transcriptional programs and that each subtype is characterized by diverse protein expression and drug responses. Single-cell analyses suggest, however, that multiple transcriptional programs may coexist within a single tumor or, even, a single cell, thus providing a potential novel mechanism for lineage switching and therapeutic resistance.

Citation Format: Carl M. Gay, Lixia Diao, C. Allison Stewart, Yuanxin Xi, Robert J. Cardnell, Stephen G. Swisher, Jack A. Roth, Bonnie S. Glisson, Jing Wang, John V. Heymach, Lauren A. Byers. Inter- and intra-tumoral variations in ASCL1, NEUROD1, and POU2F3 transcriptional programs underlie three distinct molecular subtypes of small cell lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3772.

Abstract LB-148: Combination treatment of the CHK1 inhibitor, SRA737, and low dose gemcitabine demonstrates profound synergy with anti-PDL1 inducing durable tumor regressions and modulating the immune microenvironment in small cell lung cancer

Background: Small cell lung cancer (SCLC), the most aggressive form of lung cancer, shows poor response rates to immunotherapy targeting the programmed cell death protein 1 pathway (PD-(L)1). Our group previously discovered that SCLC exhibits high expression of checkpoint kinase 1 (CHK1) and that the CHK1 inhibitor SRA737 activates the innate immune STING pathway, demonstrating robust anti-tumor activity and synergy in combination with anti-PD-L1 in an SCLC model. As SRA737 is being tested in SCLC patients in combination with low dose gemcitabine (LDG), we evaluated the efficacy and immune correlates (including macrophages associated with resistance to immune checkpoint blockade) of the SRA737+LDG regimen in combination with anti-PD-L1 in an SCLC model.

Results: Trp53, Rb1 and p130 (RPP) triple knockout SCLC cells were implanted into the flank of B6129F1 immunocompetent mice. After the mice developed tumors, they were treated with single agents or various drug combinations. Anti-PD-L1 and LDG demonstrated minimal effect on tumor growth as single agents and only a modest effect as a combination. Moderate to strong anti-tumor activity was however observed with SRA737 monotherapy which directly correlated with dosing intensity. The most profound and synergistic anti-tumor activity was observed when anti-PD-L1 was combined with the SRA737+LDG regimen, with all animals showing durable regressions. Analysis of tumor infiltrating immune cells at the end of this treatment regimen showed a dramatic induction of cytotoxic T-cells and a reduction of exhausted and regulatory T cells. Similarly, pro-inflammatory M1 type macrophages and dendritic cells were increased while immunosuppressive M2 type macrophages and MDSC cells were dramatically decreased. As monotherapy, the more dose intensive SRA737 schedule resulted in similar effects on lymphocytes when combined with anti-PD-L1. These effects are consistent with our previous data showing that SRA737 treatment leads to an induction of STING and type I interferon signaling in tumors, which is associated with the establishment of an anti-tumor immune microenvironment.

Discussion: Our findings suggest that the combination of anti-PD-L1 with the SRA737+LDG regimen may represent the optimal implementation of these agents, leading to a dramatic anti-tumor activity accompanied by the establishment of a strong anti-tumor immune microenvironment. Given that anti-PD-(L)1 drugs are approved but show limited efficacy in SCLC, our preclinical data provide a strong rationale for combining these agents with the SRA737+LDG regimen to enhance clinical response rates.

Citation Format: Triparna Sen, Carminia M. Della Corte, Snezana Milutinovic, Lixia Diao, Robert J. Cardnell, Ryan J. Hansen, Bryan Strouse, Michael P. Hedrick, Christian Hassig, Jing Wang, Lauren A. Byers. Combination treatment of the CHK1 inhibitor, SRA737, and low dose gemcitabine demonstrates profound synergy with anti-PDL1 inducing durable tumor regressions and modulating the immune microenvironment in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-148.

Differential Sensitivity Analysis for Resistant Malignancies (DISARM) Identifies Common Candidate Therapies across Platinum-Resistant Cancers

PURPOSE

Despite a growing arsenal of approved drugs, therapeutic resistance remains a formidable and, often, insurmountable challenge in cancer treatment. The mechanisms underlying therapeutic resistance remain largely unresolved and, thus, examples of effective combinatorial or sequential strategies to combat resistance are rare. Here, we present Differential Sensitivity Analysis for Resistant Malignancies (DISARM), a novel, integrated drug screen analysis tool designed to address this dilemma.

EXPERIMENTAL DESIGN

DISARM, a software package and web-based application, analyzes drug response data to prioritize candidate therapies for models with resistance to a reference drug and to assess whether response to a reference drug can be utilized to predict future response to other agents. Using cisplatin as our reference drug, we applied DISARM to models from nine cancers commonly treated with first-line platinum chemotherapy including recalcitrant malignancies such as small cell lung cancer (SCLC) and pancreatic adenocarcinoma (PAAD).

RESULTS

In cisplatin-resistant models, DISARM identified novel candidates including multiple inhibitors of PI3K, MEK, and BCL-2, among other classes, across unrelated malignancies. Additionally, DISARM facilitated the selection of predictive biomarkers of response and identification of unique molecular subtypes, such as contrasting ASCL1-low/cMYC-high SCLC targetable by AURKA inhibitors and ASCL1-high/cMYC-low SCLC targetable by BCL-2 inhibitors. Utilizing these predictions, we assessed several of DISARM's top candidates, including inhibitors of AURKA, BCL-2, and HSP90, to confirm their activity in cisplatin-resistant SCLC models.

CONCLUSIONS

DISARM represents the first validated tool to analyze large-scale in vitro drug response data to statistically optimize candidate drug and biomarker selection aimed at overcoming candidate drug resistance.

Abstract IA27: MYC drives molecular and therapeutically distinct subtype of SCLC

Small cell lung cancer (SCLC) has largely been treated in the clinic as a homogeneous disease for the last 40 years. However, it is become increasingly appreciated that SCLC exhibits both intra- and intertumoral heterogeneity. Genetic loss of the tumor suppressors RB1 and TP53 is nearly universal in SCLC, while amplifications in MYC family members including C-, L-, and N-MYC are mutually exclusive. Using genetically engineered mouse models (GEMMs), we show that MycT58A expression cooperates with Rb1 and Trp53 loss in the mouse lung to promote aggressive, highly metastatic tumors that are initially sensitive to chemotherapy followed by relapse, similar to human SCLC. Importantly, MYC drives a neuroendocrine-low ‘‘variant’’ subset of SCLC with low ASCL1 and high NEUROD1 expression corresponding to transcriptional profiles of human SCLC. The MYC-driven subset of SCLC is also low for other clinically relevant biomarkers such as TTF1/NKX2.1 and DLL3. Targeted drug screening reveals that SCLC with high MYC expression is vulnerable to Aurora kinase inhibition, which, combined with chemotherapy, strongly suppresses tumor progression and increases survival. These findings are consistent with the results of recent clinical trials in patients with relapsed SCLC who received paclitaxel with or without the AURKA inhibitor alisertib. Furthermore, recent preclinical studies demonstrate that the MYC-driven subset of SCLC is preferentially sensitive to CHK1 inhibition and other metabolic targets compared to MYCL-driven SCLC. These data identify molecular features for patient stratification and uncover potential targeted treatment approaches for MYC-driven SCLC.

Citation Format: Gurkan Mollaoglu, Matthew R. Guthrie, Stefanie Bohm, Johannes Bragelmann, Milind D. Chalishazar, Abbie S. Ireland, Fang Huang, Zeping Hu, Robert J. Cardnell, Triparna Sen, Jason Gertz, Jane E. Johnson, Adi F. Gazdar, Lauren A. Byers, Ralph J. DeBerardinis, Robert J. Wechsler-Reya, Martin Sos, Trudy G. Oliver. MYC drives molecular and therapeutically distinct subtype of SCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA27.

Randomized, Double-Blind, Phase II Study of Temozolomide in Combination With Either Veliparib or Placebo in Patients With Relapsed-Sensitive or Refractory Small-Cell Lung Cancer

Purpose Both temozolomide (TMZ) and poly (ADP-ribose) polymerase (PARP) inhibitors are active in small-cell lung cancer (SCLC). This phase II, randomized, double-blind study evaluated whether addition of the PARP inhibitor veliparib to TMZ improves 4-month progression-free survival (PFS). Patients and Methods A total of 104 patients with recurrent SCLC were randomly assigned 1:1 to oral veliparib or placebo 40 mg twice daily, days 1 to 7, and oral TMZ 150 to 200 mg/m²/day, days 1 to 5, of a 28-day cycle until disease progression, unacceptable toxicity, or withdrawal of consent. Response was determined by imaging at weeks 4 and 8, and every 8 weeks thereafter. Improvement in PFS at 4 months was the primary end point. Secondary objectives included overall response rate (ORR), overall survival (OS), and safety and tolerability of veliparib with TMZ. Exploratory objectives included PARP-1 and SLFN11 immunohistochemical expression, MGMT promoter methylation, and circulating tumor cell quantification. Results No significant difference in 4-month PFS was noted between TMZ/veliparib (36%) and TMZ/placebo (27%; P = .19); median OS was also not improved significantly with TMZ/veliparib (8.2 months; 95% CI, 6.4 to 12.2 months; v 7.0 months; 95% CI, 5.3 to 9.5 months; P = .50). However, ORR was significantly higher in patients receiving TMZ/veliparib compared with TMZ/placebo (39% v 14%; P = .016). Grade 3/4 thrombocytopenia and neutropenia more commonly occurred with TMZ/veliparib: 50% versus 9% and 31% versus 7%, respectively. Significantly prolonged PFS (5.7 v 3.6 months; P = .009) and OS (12.2 v 7.5 months; P = .014) were observed in patients with SLFN11-positive tumors treated with TMZ/veliparib. Conclusion Four-month PFS and median OS did not differ between the two arms, whereas a significant improvement in ORR was observed with TMZ/veliparib. SLFN11 expression was associated with improved PFS and OS in patients receiving TMZ/veliparib, suggesting a promising biomarker of PARP-inhibitor sensitivity in SCLC.

Dynamic variations in epithelial-to-mesenchymal transition (EMT), ATM, and SLFN11 govern response to PARP inhibitors and cisplatin in small cell lung cancer

Small cell lung cancer (SCLC) is one of the most aggressive forms of cancer, with a 5-year survival <7%. A major barrier to progress is the absence of predictive biomarkers for chemotherapy and novel targeted agents such as PARP inhibitors. Using a high-throughput, integrated proteomic, transcriptomic, and genomic analysis of SCLC patient-derived xenografts (PDXs) and profiled cell lines, we identified biomarkers of drug sensitivity and determined their prevalence in patient tumors. In contrast to breast and ovarian cancer, PARP inhibitor response was not associated with mutations in homologous recombination (HR) genes (e.g., BRCA1/2) or HRD scores. Instead, we found several proteomic markers that predicted PDX response, including high levels of SLFN11 and E-cadherin and low ATM. SLFN11 and E-cadherin were also significantly associated with in vitro sensitivity to cisplatin and topoisomerase1/2 inhibitors (all commonly used in SCLC). Treatment with cisplatin or PARP inhibitors downregulated SLFN11 and E-cadherin, possibly explaining the rapid development of therapeutic resistance in SCLC. Supporting their functional role, silencing SLFN11 reduced in vitro sensitivity and drug-induced DNA damage; whereas ATM knockdown or pharmacologic inhibition enhanced sensitivity. Notably, SCLC with mesenchymal phenotypes (i.e., loss of E-cadherin and high epithelial-to-mesenchymal transition (EMT) signature scores) displayed striking alterations in expression of miR200 family and key SCLC genes (e.g., NEUROD1, ASCL1, ALDH1A1, MYCL1). Thus, SLFN11, EMT, and ATM mediate therapeutic response in SCLC and warrant further clinical investigation as predictive biomarkers.

Protein expression of TTF1 and cMYC define distinct molecular subgroups of small cell lung cancer with unique vulnerabilities to aurora kinase inhibition, DLL3 targeting, and other targeted therapies

Small cell lung cancer (SCLC) is a recalcitrant cancer for which no new treatments have been approved in over 30 years. While molecular subtyping now guides treatment selection for patients with non-small cell lung cancer and other cancers, SCLC is still treated as a single disease entity. Using model-based clustering, we found two major proteomic subtypes of SCLC characterized by either high thyroid transcription factor-1 (TTF1)/low cMYC protein expression or high cMYC/low TTF1. Applying "drug target constellation" (DTECT) mapping, we further show that protein levels of TTF1 and cMYC predict response to targeted therapies including aurora kinase, Bcl2, and HSP90 inhibitors. Levels of TTF1 and DLL3 were also highly correlated in preclinical models and patient tumors. TTF1 (used in the diagnosis lung cancer) could therefore be used as a surrogate of DLL3 expression to identify patients who may respond to the DLL3 antibody-drug conjugate rovalpituzumab tesirine. These findings suggest that TTF1, cMYC or other protein markers identified here could be used to identify subgroups of SCLC patients who may respond preferentially to several emerging targeted therapies.

A phase 2, open-label, multi-center study of amuvatinib in combination with platinum etoposide chemotherapy in platinum-refractory small cell lung cancer patients

Background

Amuvatinib (MP-470) is a multi-targeted kinase inhibitor with potent activity against c-Kit, synergistic with DNA-damaging agents. We evaluated amuvatinib in combination with platinum-etoposide (EP) chemotherapy by objective response rate, survival, and tolerability in platinum-refractory small cell lung cancer (SCLC) patients.

Methods

This study used a Simon 2-stage design requiring ≥3 centrally confirmed responses in the first 21 subjects. Subjects received EP with 300 mg amuvatinib orally three times daily in cycles of 21 days. A three-day amuvatinib run-in period before EP occurred in Cycle 1. Subjects received the same EP chemotherapy regimen given prior to progression/relapse.

Results

Among 23 subjects treated, we observed four PRs (17.4%) per RECIST 1.1, only two of which were centrally confirmed (8.7%, response duration 119, 151 days). Three subjects (13%) had confirmed stable disease. c-Kit H-score was ≥100 in two subjects whose respective durations of disease control were 151 and 256 days.

Conclusions

The addition of amuvatinib to EP chemotherapy in unselected, platinum-refractory SCLC did not meet the primary endpoint of ≥3 confirmed responses in stage 1. However, high c-Kit expression in two subjects with durable disease control suggests the potential for further study of amuvatinib in SCLC patients with high c-Kit expression.

Abstract 1560: Differential sensitivity analysis for resistant malignancies (DISARM), a novel approach for drug screen analysis, identifies common candidate drugs across platinum-resistant cancer types

Resistance to therapy, including conventional chemotherapy, targeted therapy and immunotherapy, continues to plague cancer treatment. Moreover, mechanisms governing resistance are poorly characterized leading to a dearth of rational combinatorial and sequential treatment strategies. While drug response data is abundant across myriad tumor types and drug classes, there exists no high-throughput method to probe such data with a query as simple as “If tumors are resistant to drug X, to what drug(s) are they sensitive?”- a seemingly trivial problem beset by immense data sets and imprecise definitions of sensitivity and resistance. Here, we present DISARM, a novel approach designed specifically to screen for drugs that are active in spite of resistance to a reference drug. DISARM selects candidates based on the proportion of samples that are resistant to a reference drug but sensitive to a candidate drug with simultaneous consideration to relatively lower IC50 values for candidate drugs and higher IC50 values for reference drugs. As candidates may work in only a subset of resistant models and precise delineation between sensitivity and resistance may vary between experimental settings, DISARM permits flexibility in dichotomizing drug data and uses grid search to optimize specifications. To illustrate, we analyzed publically available cell line data (IC50 data) from several cancer types for which platinum-based therapy is a standard of care, identifying multiple drugs that demonstrate activity in cisplatin-resistant models across tumor types such as the BCL-2 inhibitor obatoclax in small cell lung cancer, lung adenocarcinoma, gastric adenocarcinoma and bladder cancer, and the farnesyltransferase inhibitor tipifarnib in small cell lung cancer, bladder cancer, esophageal cancer, colon adenocarcinoma and head and neck squamous cell carcinoma. Frequently, multiple drugs from the same class were selected by DISARM for a single tumor type and, in these cases, we found statistically significant similarity between sensitive cell lines suggesting a subset of cisplatin-resistant cell lines that are repeatedly sensitive to a drug class. While translating preclinical observations into approved clinical use is often thwarted by an inability to identify predictive biomarkers, DISARM also allows us to select cell lines that are especially sensitive to candidate drugs or drug classes on which to perform biomarker analysis. To demonstrate this approach, we chose drugs with activity in multiple cancer types and compared mRNA and protein expression data to highlight potentially novel common and tumor-specific biomarkers for concomitant candidate drug sensitivity and cisplatin resistance. Thus, DISARM offers a simple yet effective approach for both drug and biomarker discovery within a specified clinical niche.

Citation Format: Carl M. Gay, Pan Tong, Robert J. Cardnell, Xiao Su, Nene N. Kalu, Upasana Banerjee, Rasha O. Bara, Faye M. Johnson, John V. Heymach, Jing Wang, Lauren A. Byers. Differential sensitivity analysis for resistant malignancies (DISARM), a novel approach for drug screen analysis, identifies common candidate drugs across platinum-resistant cancer types [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 1560. doi:10.1158/1538-7445.AM2017-1560

Abstract 3887: Proteomic profiling identifies cMyc and TTF1 as biomarkers of response to the aurora kinase inhibitor alisertib in small cell lung cancer (SCLC)

Background: Small cell lung cancer (SCLC) is the most aggressive form of lung cancer, with a 5-year survival rate of only 6%. The treatment of SCLC has not changed in over 25 years, hence the development of new drugs for SCLC represents a major unmet need. A recent phase II trial of the aurora kinase inhibitor alisertib showed single agent activity in a subset (21%) of SCLC (Melichar et al, 2015) and a second study is underway testing alisertib in combination with chemotherapy (NCT02038647). However, there are currently no established biomarkers to identify patients likely to have the greatest benefit from alisertib. We have previously demonstrated the utility of proteomic profiling to identify targets and markers in SCLC. Here we use proteomics to identify markers of response to alisertib in SCLC.

Methods: The sensitivity (IC50) of 51 SCLC cell lines to alisertib was assayed in 5-day proliferation assays. Expression levels of 171 total and/or phosphorylated proteins were measured by reverse phase protein array (RPPA) and correlated with IC50’s. Using two approaches – 1) Spearman correlation of IC50 to protein data for all cell lines and 2) t-test comparing protein data between the most and least sensitive cell lines – we generated consensus markers of response.

Results: Proliferation assays showed sensitivity to alisertib at clinically achievable doses in 14/51 (27%) cell lines (based on Cmax = 1.8uM, Phase I single agent trial). High cMyc protein was the top marker of sensitivity to alisertib (R = -0.47, p = 0.0006 as continuous variables; fold difference = 3.52, p = 0.008 by t-test comparing extremes). Further analysis revealed a bi-modal distribution of cMyc protein, defined as high and low using a bimodality index. The cMyc protein high group (25%) included cell lines that were both cMyc amplified and non-amplified. While cMyc amplified cell lines (11%) are more sensitive to alisertib than non-amplified (p = 0.002), high cMyc protein captures a larger population of SCLC that is sensitive to alisertib.

In contrast, expression of thyroid transcription factor 1 (TTF1, a standard IHC marker used in the diagnosis of lung cancer) was the top marker of alisertib resistance (R = 0.38, p = 0.006; fold difference = -4.22, p = 0.003). TTF1 protein expression was also bi-modal, with 32% of cell lines falling into a distinct TTF1-low (more sensitive to alisertib) group.

Conclusions: High cMyc and low TTF1 protein expression identify a subset of SCLC cell lines (27%) that are sensitive to single agent alisertib. cMyc protein as a marker of response is consistent with other preclinical findings suggesting that cMyc amplified SCLC may be more sensitive to aurora kinase inhibition. The association of low TTF1 expression with alisertib sensitivity may prove to be of particular value in selecting patients for treatment given that immunohistochemical assessment of TTF1 is commonly used in the diagnosis of SCLC.

Citation Format: Robert J. Cardnell, Lerong Li, Fatemeh Masrorpour, Huifeng Niu, Jeffrey Ecsedy, Jing Wang, Lauren A. Byers. Proteomic profiling identifies cMyc and TTF1 as biomarkers of response to the aurora kinase inhibitor alisertib in small cell lung cancer (SCLC). [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 3887.

A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition

PURPOSE

We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature.

EXPERIMENTAL DESIGN

Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated.

RESULTS

Compared with the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets, such as PD1, PD-L1, CTLA4, OX40L, and PD-L2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by IHC in an independent lung cancer cohort.

CONCLUSIONS

This new signature provides a novel, patient-based, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints.

Abstract 5316: Check point kinase 1 (Chk1) targeting as a novel therapeutic strategy in small cell lung cancer (SCLC)

Background: Small cell lung cancer (SCLC) is the most aggressive form of lung cancer, accounting for 14% of lung cancers. It is associated with poor outcomes and few effective treatments. Identification of novel therapeutic targets is imperative for improving treatment outcomes. In our previous work we identified several DNA repair proteins including check point kinase 1 (Chk1) and poly (ADP-ribose) polymerase 1 (PARP1) that are overexpressed in SCLC and are high priority candidate targets. TP53-mutant cells (a hallmark of SCLC) rely on Chk1 to arrest the S and G2 phases of the cell cycle. Hence, inhibition of Chk1 in p53 mutant cells abrogates the S and G2 checkpoints driving such cells to mitotic catastrophe and apoptosis. In this study we tested the in vitro efficacy of Chk1 inhibitors as single agents and in combination with a PARP1 inhibitor and cisplatin.

Experimental design: SCLC cell lines [human cell lines plus those from a patient derived xenograft (PDX) and genetically engineered mouse models (GEMMs)] were treated with Chk1 inhibitors (SCH900776, LY2603618, LY2606368) alone and in combination with olaparib (PARP inhibitor) or cisplatin. Cell proliferation was measured by Cell Titer Glo assay. Drug sensitivity (IC50) was correlated with baseline expression levels of &gt;190 total or phosphorylated proteins measured by reverse phase protein array (RPPA) to identify potential predictive markers.

Result: Single-agent Chk1 suppression decreased proliferation of SCLC cells in a dose-dependent manner. SCLC lines exhibited varied levels of sensitivity to the Chk1 inhibitors, with greatest single agent activity observed with LY2606368 (IC50 2-30nM). LY2606368 also showed appreciable single agent activity in PDX and GEMM-derived cell lines (IC50 2-7nM). Single agent activity was also observed with the other Chk1 inhibitors (SCH900776 IC50 0.3-10uM; LY2603618 IC50 0.2-10uM). Combination of LY2606368 with olaparib and cisplatin revealed an additive effect. Proteomic analysis revealed an association between Chk1 inhibitor sensitivity and elevated basal expression of pro-apoptotic proteins (cleaved PARP, Bax, and Caspase 3; p &lt;0.05). In contrast, Chk1 resistance was associated with higher levels of PI3K pathway proteins (pAkt, pGSK, p &lt;0.05).

Conclusion: Identification and characterization of novel therapeutic targets is essential to improve efficacy of SCLC therapy. In this preliminary study we tested Chk1 inhibitors as potential therapies in SCLC and provide evidence that targeting Chk1 could be a promising therapeutic strategy for SCLC. Further preclinical and clinical investigation is needed to confirm the molecular mechanism and in vivo outcome of Chk1 targeting.

Acknowledgement: 1. 2013 NCI Cancer Clinical Investigator Team Leadership Award, P30 CA016672 (Byers) 2. UT MD Anderson Small Cell Lung Cancer Working Group and Abell Hangar Foundation Distinguished Professor Endowment (Glisson).

Citation Format: Aly A. Valliani, Triparna Sen, Fatehmeh Masrorpour, Lixia Diao, Robert J. Cardnell, Jing Wang, Bonnie S. Glisson, Helen Piwnica-Worms, Don L. Gibbons, Lauren A. Byers. Check point kinase 1 (Chk1) targeting as a novel therapeutic strategy in small cell lung cancer (SCLC). [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 5316. doi:10.1158/1538-7445.AM2015-5316

Abstract 7: PARP and Bcl-2 co-inhibition in small cell lung cancer (SCLC)

Background: Small cell lung cancer (SCLC) accounts for 10-15% of all lung cancers. SCLC is initially responsive to chemotherapy, but quickly relapses. With few other treatment options available, the 5-year survival rate remains less than 5%. Bcl-2 is an anti-apoptotic protein that is overexpressed in SCLC and is associated with chemotherapy resistance. Previous studies have shown Bcl-2 inhibition to be effective in SCLC cell lines; however, Bcl-2 antagonists, such as GX15-070 (obatoclax mesylate), have been disappointing in clinical trials. We have recently shown that PARP-1, a DNA binding protein involved in single and double strand break repairs, is overexpressed in SCLC and that SCLC models are sensitive to PARP inhibition. As recent work illustrated a synergistic interaction between Bcl-2 antagonists and PARP inhibitors in pancreatic cancer cell lines, we hypothesize that a similar effect may occur in SCLC.

Methods: Thirteen SCLC cell lines were treated with GX15-070 ± the PARP inhibitor AZD2281 (olaparib), and proliferation was assayed by CellTiter-Glo. In an effort to identify potential biomarkers of response to combination therapy, drug sensitivities (IC50 values) were correlated with proteomic profiling data generated by reverse phase protein array (RPPA), which measured the expression of 193 total and/or phospho-proteins.

Results: As expected, SCLC cell lines exhibited a range of sensitivities to single agent GX15-070 in vitro (0.02-0.40 μM). When AZD2281 (PARP inhibitor) was added to a low dose of GX15-070 (0.03 μM), an additive effect was observed in 6 of 10 cell lines tested. Baseline proteomic profiling by RPPA revealed a number of proteins that correlated with sensitivity to Bcl-2 inhibition, including a pathway connecting high insulin receptor substrate-1 (IRS) to high Bcl-xL, (IRS-1, SGK, FOXO3, BIM, and Bcl-xL). Bcl-xL is also a target of GX15-070.

Conclusion: Some SCLC cell lines were sensitive to Bcl-2 inhibition. In contrast to pancreatic cancer, a synergistic interaction was not observed when GX15-070 was combined with AZD2281. This combination showed at best an additive interaction in 6 of 10 SCLC cell lines tested, indicating limited value to the SCLC patient population as a whole. Interestingly, high IRS-1 and Bcl-xL expression may serve as biomarkers of response to GX15-070, suggesting a subset of SCLC patients that may be more sensitive to Bcl-2 inhibition. Our baseline proteomic analysis also suggests novel Bcl-2 inhibitor combinations. Metformin, for example, elevates expression of IRS-1, and its use could further sensitize SCLC to Bcl-2 inhibition. We are currently testing this novel combination in pre-clinical models of SCLC

Citation Format: Janaya Shelly, Robert J. Cardnell, Fatemeh Masrorpour, Lixia Diao, Jing Wang, Lauren Byers. PARP and Bcl-2 co-inhibition in small cell lung cancer (SCLC). [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 7. doi:10.1158/1538-7445.AM2015-7

Abstract 2961: Characterization of methylation profiles reveals distinct epigenomic patterns in SCLC and NSCLC

Background: Small cell lung cancer (SCLC) is a highly lethal malignancy characterized by rapid growth, early metastasis and poor prognosis. SCLC shows distinct molecular and clinical features when compared to other lung cancer subtypes. Previous analyses by us and others have identified genomic and proteomic differences between SCLC and Non-Small Cell Lung Cancer (NSCLC). Epigenetic alterations are some of the earliest events that could also lead to oncogenic changes and thus play an essential role in tumor initiation and progression. However, epigenetic differences between SCLC and NSCLC contributing to the alterations in gene and protein expression patterns, distinct biological features and therapeutic response have not been well characterized. Here, we investigate the differences in the methylation patterns of SCLC and NSCLC to provide novel insights into epigenetic associated gene alterations to identify potential therapeutic targets in SCLC.

Material and Methods: A genome-wide DNA methylation profiling of SCLC and NSCLC cell lines was used for this investigation. We correlated DNA methylation status with gene expression and protein expression levels in 31 SCLC and 73 NSCLC lines to identify the relationship of epigenetic with genomic and proteomic features distinguishing SCLC from NSCLC.

Results: SCLC and NSCLC lines exhibited different methylation profiles and we identified 484 genes that had a significant inverse correlation between methylation status and mRNA expression levels (Rho ≤ -0.5 and FDR = 0.01), (“genes regulated by methylation,” GRM) that distinguished SCLC from NSCLC. Ingenuity pathway analysis of the 484 genes identified significant associations with neuregulin signaling, immune trafficking, integrin signaling, glioma invasiveness canonical pathways. Proteomic profiling by Reverse Phase Protein Array (RPPA) validated the different expression of some of the 484 genes identifying nine that were hypermethylated and downregulated at protein levels in SCLC compared to NSCLC lines (PTEN, CyclinD1, Caveolin, Notch3, TAZ, HSP27, STAT6 and both total and phosphorylated levels of receptor tyrosine kinases such Her2 and, MET).

Conclusions: Genome wide methylation, mRNA expression, and detailed proteomic analyses have identified specific epigenic differences between SCLC and NSCLC that impact on important signaling pathways including widespread loss of PTEN function and receptor tyrosine kinase (RTK) expression in SCLCs which need to be considered in developing new rationale therapies for SCLC.

Citation Format: Seema Mukherjee, Bonnie S. Glisson, John D. Minna, Robert J. Cardnell, Luc Girard, Adi Gazdar, Lixia Diao, Jing Wang, Lauren A. Byers. Characterization of methylation profiles reveals distinct epigenomic patterns in SCLC and NSCLC. [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 2961. doi:10.1158/1538-7445.AM2015-2961

The Role of Nitric Oxide Synthase Uncoupling in Tumor Progression

Here, evidence suggests that nitric oxide synthases (NOS) of tumor cells, in contrast with normal tissues, synthesize predominantly superoxide and peroxynitrite. Based on high-performance liquid chromatography analysis, the underlying mechanism for this uncoupling is a reduced tetrahydrobiopterin:dihydrobiopterin ratio (BH4:BH2) found in breast, colorectal, epidermoid, and head and neck tumors compared with normal tissues. Increasing BH4:BH2 and reconstitution of coupled NOS activity in breast cancer cells with the BH4 salvage pathway precursor, sepiapterin, causes significant shifts in downstream signaling, including increased cGMP-dependent protein kinase (PKG) activity, decreased β-catenin expression, and TCF4 promoter activity, and reduced NF-κB promoter activity. Sepiapterin inhibited breast tumor cell growth in vitro and in vivo as measured by a clonogenic assay, Ki67 staining, and 2[18F]fluoro-2-deoxy-D-glucose-deoxyglucose positron emission tomography (FDG-PET). In summary, using diverse tumor types, it is demonstrated that the BH4:BH2 ratio is lower in tumor tissues and, as a consequence, NOS activity generates more peroxynitrite and superoxide anion than nitric oxide, resulting in important tumor growth-promoting and antiapoptotic signaling properties.

IMPLICATIONS

The synthetic BH4, Kuvan, is used to elevate BH4:BH2 in some phenylketonuria patients and to treat diseases associated with endothelial dysfunction, suggesting a novel, testable approach for correcting an abnormality of tumor metabolism to control tumor growth.

Proteomic markers of DNA repair and PI3K pathway activation predict response to the PARP inhibitor BMN 673 in small cell lung cancer

PURPOSE

Small cell lung carcinoma (SCLC) is an aggressive malignancy affecting nearly 30,000 people annually in the United States. We have previously identified elevated PARP1 levels in SCLC and demonstrated in vitro sensitivity to the PARP inhibitors AZD 2281 and AG014699. Here, we evaluate activity of a novel, potent PARP inhibitor, BMN 673, and identify markers of response as a basis for developing predictive markers for clinical application.

EXPERIMENTAL DESIGN

Inhibition of SCLC proliferation by BMN 673 was assayed in vitro and effects on tumor growth were measured in SCLC xenograft models. Protein expression and pathway activation was assessed by reverse phase protein array and western blot analysis. PARP inhibition was confirmed using a PAR ELISA.

RESULTS

We demonstrate striking, single agent activity of BMN 673 in SCLC cell lines and xenografts, with single agent BMN 673 exhibiting in vivo activity similar to cisplatin. Sensitivity to BMN 673 was associated with elevated baseline expression levels of several DNA repair proteins, whereas greater drug resistance was observed in SCLC models with baseline activation of the PI3K/mTOR pathway. Furthermore, we developed and confirmed these data with a novel "DNA repair score" consisting of a group of 17 DNA repair proteins.

CONCLUSIONS

Elevated expression of multiple DNA repair proteins, as well as a corresponding "DNA repair protein score," predict response to BMN 673 in in vitro SCLC models. These observations complement recent work in which PI3K inhibition sensitizes breast cancer models to PARP inhibition, suggesting cooperation between DNA repair and PI3K pathways.

Abstract 2489: Proteomic profiling identifies PI3K and DNA repair pathways as potential markers of response to PARP inhibitor BMN673 in SCLC

Background: Small cell lung cancer (SCLC) is an aggressive malignancy that accounts for 13% of lung cancers in the US and has a 5-year survival rate &lt;10%. Novel therapeutic approaches are critically needed to improve clinical outcomes. Using proteomic profiling, we previously identified high levels of PARP1 expression in SCLC cell lines and tumors. We also demonstrated in vitro sensitivity of SCLC to two PARP inhibitors, olaparib and rucaparib. Here we explore markers of response and pathways modulated following PARP1 inhibition as a basis for developing potential predictive markers and rational drug combinations.

Methods: Sensitivity of SCLC lines to BMN673 and cisplatin was determined by CellTiter-Glo cell viability assay. Total and phospho-protein expression of 200 markers was measured at baseline and following drug treatment in SCLC cell lines by reverse phase protein array (RPPA). Correlations between baseline protein expression and drug sensitivity were determined by Spearman rank correlation. Modulation of protein expression post treatment was assessed by ANOVA.

Results: The novel PARP inhibitor BMN673 had potent in vitro activity in a panel of 12 SCLC cell lines with IC50’s ranging from 1.7-15nM. A higher expression level of several DNA repair proteins was associated with greater BMN673 sensitivity. For example, protein expression levels of ERCC1, DNA PKcs, ATM, FANCD2, and pChk2 were inversely correlated with IC50 values (Rho values -0.93 to -0.81; p≤0.02). In contrast, high baseline expression of phosphorylated Akt (T308) (R=0.91, p=0.005) and pAkt (S473) (R=0.81, p=0.02) were associated with decreased sensitivity to BMN673. We also observed increased phosphorylation of mTOR, Akt, and S6 (p&lt;0.02) at 24h following PARP inhibitor treatment, suggesting that PI3K/Akt/mTOR pathway activation may be associated with both inherent and acquired resistance. Consistent with clinical studies suggesting greater PARP inhibitor activity in platinum-sensitive tumors, markers of BMN673 response overlapped with markers of cisplatin sensitivity, with higher DNA repair protein levels and lower pAkt levels associated with greater cisplatin activity in vitro in the same SCLC cell line panel.

Conclusions: Here we demonstrate significant, single-agent in vitro activity of the PARP inhibitor BMN673 in SCLC and potential predictive markers of response. Interestingly, for the first time we show an inverse correlation between PARP inhibitor sensitivity and PI3K/Akt/mTOR pathway activation. This observation parallels recent data suggesting that PI3K inhibition may sensitize breast cancer to PARP inhibition and suggests a potential coordinated regulation between DNA repair and PI3K pathways. The activity of BMN673 and these candidate response biomarkers will be further investigated in a Phase I cohort expansion of BMN673 in patients with SCLC.

Citation Format: Robert J. Cardnell, Ying Feng, Lixia Diao, You Hong Fan, Jing Wang, Yuqiao Shin, John D. Minna, John V. Heymach, Lauren A. Byers. Proteomic profiling identifies PI3K and DNA repair pathways as potential markers of response to PARP inhibitor BMN673 in SCLC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2489. doi:10.1158/1538-7445.AM2013-2489