Abstract CT024: Durvalumab (D) + platinum-etoposide (EP) in 1L extensive-stage small-cell lung cancer (ES-SCLC): Exploratory analysis of SCLC molecular subtypes in CASPIAN

Background: In the Phase 3 CASPIAN study, 1L D+EP significantly improved OS vs EP in pts with ES-SCLC with benefit sustained after >3 years of median follow-up (HR 0.71; 95% CI 0.60-0.86; nominal p=0.0003; median OS [mOS] 12.9 mos vs 10.5 mos). 4 SCLC subtypes with distinct therapeutic vulnerabilities were recently identified using 2 different methods (Rudin et al, 2019; Gay et al, 2021) based on differential gene expression. In this exploratory analysis using RNA sequencing (RNAseq) data from CASPIAN, we explored the concordance between the 2 methods and the association of subtypes with OS.

Methods: Pts with ES-SCLC received 4 cycles of D+EP followed by maintenance D; or up to 6 cycles of EP. RNAseq data were generated from FFPE tumor samples collected at screening. Data cutoff: Mar 22, 2021.

Results: 57/268 (21.3%) pts in the D+EP arm and 47/269 (17.5%) pts in the EP arm had RNAseq data (biomarker-evaluable population; BEP). In the BEP, the % of pts with WHO PS 1 was slightly higher and the % with brain metastases slightly lower at baseline vs the ITT population. In the BEP, mOS was 11.8 mos in the D+EP arm vs 9.1 mos in the EP arm (HR 0.61; 95% CI 0.40-0.92). Prevalence of neuroendocrine (ASCL1 and NEUROD1) and non-neuroendocrine subtypes (POU2F3 and YAP1 [Rudin] or Inflamed [Gay]) was similar using both methods (Table). However, ASCL1 was more prevalent and NEUROD1 less prevalent with the Rudin method. Inflamed and YAP1 subtypes (11% and 8% prevalence) showed high concordance between methods. Using either method, the mOS in the D+EP arm was higher in the Inflamed or YAP1 subtype vs the other 3 subtypes (Table). Analysis of OS by gene signature will be presented.

Conclusions: Among the 4 subtypes, the Inflamed or YAP1 subtype showed the longest OS in the D+EP arm, suggesting this may represent a subgroup primed to respond to immunotherapy. Despite the limited sample size, this finding is consistent with other studies.

mOS (95% CI) Rudin et al, 2019 ASCL1 NEUROD1 POU2F3 YAP1* D+EP (n=50) (n=1) (n=2) (n=4) 11.5 (8.4-14.9) 9.5 (NE-NE) 4.8 (2.9-NE) 17.3 (12.8-NE) EP (n=38) (n=2) (n=3) (n=4) 10.7 (8.1-12.4) 7.1 (4.8-NE) 6.1 (1.3-NE) 6.9 (4.5-NE) Gay et al, 2021 ASCL1 NEUROD1 POU2F3 Inflamed D+EP (n=21) (n=25) (n=5) (n=6) 9.5 (6.1-14.9) 14.6 (8.6-16.6) 6.8 (2.9-NE) 17.6 (11.4-NE) EP (n=16) (n=19) (n=7) (n=5) 8.3 (3.0-15.1) 10.5 (7.9-13.6) 7.5 (1.3-10.2) 11.3 (6.3-NE) *A sample is assigned as YAP1 subtype per Rudin et al, 2019, when expression of YAP1 is higher than that of ASCL1, NEUROD1 and POU2F3; NE, not estimable

Citation Format: Mingchao Xie, Priti Chugh, Helen Broadhurst, Zhongwu Lai, David Whitston, Luis Paz-Ares, Carl Gay, Lauren Byers, Charles M. Rudin, Ross Stewart, J. Carl Barrett, Yashaswi Shrestha. Durvalumab (D) + platinum-etoposide (EP) in 1L extensive-stage small-cell lung cancer (ES-SCLC): Exploratory analysis of SCLC molecular subtypes in CASPIAN [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 CT024.

Abstract 390: Identification of a novel immunosuppressive myeloid gene expression signature for clinical biomarker development

Cell-type abundance GE signatures are useful for informing drug mechanism of action and may be useful in-patient selection for cancer immunotherapies. Recently, we validated natural killer cell- and dendritic cell-type specific expression signatures using a tiered strategy that included both computational and ex vivo validation. Here, we built upon this strategy to validate expression signatures for immunosuppressive myeloid cells (IMC). IMC play a critical role in impairing anti-tumor immunity and increased levels of peripheral IMC have been associated with advanced tumor progression and poor prognosis in various cancers. However, their low abundance in normal tissues and heterogeneous surface expression render their profiling difficult. To address this, we focused on validating GE signatures for IMC abundance using mRNA expression methods which are more clinically tractable than established flow cytometry methods that require intact cells.

We implemented a three-stage GE signature validation strategy. First, we generated GE data from human ex vivo differentiated IMC (LIN- CD11B+ CD33+ HLADR-). Then, we evaluated the concordance of 16 previously published myeloid signatures with cell type abundance in a series of spike-ins with varying but known quantities of ex vivo differentiated IMC in a background of undifferentiated peripheral blood mononuclear cells (PBMCs). Gene-set variation analysis (GSVA) was used to score the signatures and Spearman's rank (rS) correlation coefficient was calculated to assess the significance of correlations between GSVA scores and IMC abundance. With this method, we validated 3 of the 16 published myeloid signatures (1. MacB3/PMID:26873985 (rS = 0.87; p = 8.8e-07); 2. MacB2_3w/PMID:26873985 (rS = 0.83; p = 6.7e-06); 3. TAM/PMID:27424807 (rS = 0.80; p= 2.6e-05)).

Next, we generated a ‘de novo' signature by performing differential GE analysis and identified up-regulated genes in IMC in comparison to PBMCs with log2 fold change &gt 2, p-adj &lt 0.05). We further refined this list by selecting genes with significant concordance to IMC abundance (rS &gt 0.80, p-adj &lt 0.05) and confirmed their specificity to IMC in published scRNAseq studies [PMID: 30979687; 31033233; 32302573]. This led to a 6-gene ‘de novo' signature (MRC1, APOE, C1QA, C1QB, MMP9, SPP1) associated with IMC function with highly significant concordance (rS = 0.96; p = 1.2e-11) to IMC abundance.

Lastly, we showed that in whole blood baseline samples from HNSCC patients (n=53) treated with danvatirsen + durvalumab [NCT02499328], our ‘de novo' signature was significantly elevated (p=0.033) in patients with progressive disease compared to complete responders. Application to additional studies will be required to more fully determine its clinical utility.

Citation Format: Srimathi S. Srinivasan, Gozde Kar, Deanna L. Russell, Peter Gathungu, Minoo Rafati, David Whitston, Grant Duclos, Ben Sidders, J Carl Barrett, Tim Slidel, Patricia McCoon. Identification of a novel immunosuppressive myeloid gene expression signature for clinical biomarker development [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 390.

Generation of stable PDX derived cell lines using conditional reprogramming

Efforts to develop effective cancer therapeutics have been hindered by a lack of clinically predictive preclinical models which recapitulate this complex disease. Patient derived xenograft (PDX) models have emerged as valuable tools for translational research but have several practical limitations including lack of sustained growth in vitro. In this study, we utilized Conditional Reprogramming (CR) cell technology- a novel cell culture system facilitating the generation of stable cultures from patient biopsies- to establish PDX-derived cell lines which maintain the characteristics of the parental PDX tumor. Human lung and ovarian PDX tumors were successfully propagated using CR technology to create stable explant cell lines (CR-PDX). These CR-PDX cell lines maintained parental driver mutations and allele frequency without clonal drift. Purified CR-PDX cell lines were amenable to high throughput chemosensitivity screening and in vitro genetic knockdown studies. Additionally, re-implanted CR-PDX cells proliferated to form tumors that retained the growth kinetics, histology, and drug responses of the parental PDX tumor. CR technology can be used to generate and expand stable cell lines from PDX tumors without compromising fundamental biological properties of the model. It offers the ability to expand PDX cells in vitro for subsequent 2D screening assays as well as for use in vivo to reduce variability, animal usage and study costs. The methods and data detailed here provide a platform to generate physiologically relevant and predictive preclinical models to enhance drug discovery efforts.

Abstract LB-249: Examination of analytical factors impacting concordance of plasma-tumor testing by next-generation sequencing (NGS)

The increased usage of circulating tumor DNA (ctDNA) sequencing for oncology clinical research demonstrates a critical need for sensitive and specific testing. While we have observed a high degree of concordance between single tumor mutations in tumor and plasma, several recent studies have highlighted a lack of concordance between plasma and tumor panel NGS gene panel testing due to biological and technical factors. To explore further these factors and benchmark ctDNA NGS testing services, a set of matched plasma, tumor, and normal samples from 24 subjects were acquired from three biobanking companies. Replicate 2 ml-plasma samples were tested by four ctDNA sequencing companies, and matching tumor/normal samples were tested by two tumor sequencing companies. Concordance was measured by comparing plasma mutations to tumor mutations as well as comparing mutations among the same plasma tested by the ctDNA companies. While our experience with NGS of matched samples from clinical trials typically identifies ~30% of patients with no detectable mutation and therefore likely not shedding tumor DNA, with the retrospectively collected commercial samples ~60% lacked detectable high confidence mutations, likely due to quality control issues with sample collection. We also found variation in the concordance of ctDNA mutation detection rates among the four vendors, due to significant differences in DNA yield and assay sensitivity. While factors such as tumor heterogeneity and timing of plasma-tumor collection can lower concordance rates, the majority of discordance in our study was due to technical rather than biological variation. Assay analytical variance and the impact of reporting false positive variants are key factors that need to be addressed as plasma-based NGS testing is more widely incorporated into translational and clinical research. Examples illustrating the complexity of the analyses and giving support for confidence in ctDNA testing results will be given.

Citation Format: Daniel Stetson, Brian Dougherty, Ambar Ahmed, Tristan Lubinski, Aleksandra Markovets, Kenneth Thress, Robert McEwen, Gaia Schiavon, David Whitston, Barrett Nuttall, J. Carl Barrett. Examination of analytical factors impacting concordance of plasma-tumor testing by next-generation sequencing (NGS) [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 LB-249. doi:10.1158/1538-7445.AM2017-LB-249

Abstract 641: Use of conditional reprogramming to develop and characterize cell cultures from patient-derived xenograft (PDX) models of human lung and ovarian cancer

Patient-derived xenografts (PDX) are widely recognized as a more physiologically relevant preclinical model to standard cell line xenografts. PDX models faithfully recapitulate the original patient genetic profile, gene expression patterns and tissue histology. Despite their benefits, PDX models are limited by their inherent variability, lower throughput and lack of growth in vitro. The ability to generate cell lines from PDX models would enable high throughput chemosensitivity screens, ex vivo genetic manipulation and the development of novel orthotopic models. Development of stable PDX cell lines remains a challenge due to murine stromal outgrowth, lineage commitment and limited differentiation potential. Conditional reprogramming (CR) cell technology is a novel cell culture system facilitating the generation of stable cultures without genetic manipulation (Liu, Am J Pathol, 2012). The success of CR cell technology is dependent upon the combination of feeder cell-derived factors and Rho Kinase (ROCK) inhibitor. CR cells, therefore, represent a new class of progenitor-like cells, distinct from the phenotype of embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. The purpose of this study was to identify the advantages, limitations and potential applications of CR technology for derivation of PDX explant cell lines. Early passage human lung and ovarian PDX tumors were cultured in CR conditions to create stable explant cell lines. Cell lines were established from 5/8 (63%) PDX tumors and were expanded over 6 months in culture with varying morphologies and growth kinetics. Due to normal outgrowth of murine stromal cells, early CR cultures contained mixed populations and required murine depletion to enrich for human cells. Key oncogenic mutations in a model of ovarian papillary serous adenocarcinoma were preserved in the enriched tumor cell population. While purified CR PDX cell lines were amenable to high throughput chemosensitivity screens, in vitro chemosensitivity did not consistently predict response in in vivo murine models. The CR PDX cell lines were additionally assessed for genetic manipulation and ability to form tumors in vivo. Collectively, these results demonstrate the applications of CR technology for the generation of stable explant cell lines from PDX models for preclinical studies.

Citation Format: Alexandra Borodovsky, Travis J. McQuiston, Brian Dougherty, Ambar Ahmed, David Whitston, Daniel Stetson, Gretchen K. Hubbard, Sharon S. Challberg, Brian A. Pollok, Celina M. D’Cruz. Use of conditional reprogramming to develop and characterize cell cultures from patient-derived xenograft (PDX) models of human lung and ovarian cancer. [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 641.

Abstract 3910: Lead optimization of a series of 5-aminopyrazol-imidazopyridine compounds as potent anaplastic lymphoma kinase inhibitors active against clinically relevant ALK mutations

Despite the success of Crizotinib in treating NSCLC patients with EML4-ALK fusions, cancers eventually develop resistance via a variety of mechanisms including mutations in the ATP binding site of the kinase domain. A series of 5-aminopyrazol-imidazopyridine compounds were identified to potently inhibit anaplastic lymphoma kinase and were found to be active against a number of mutations in vitro but suffered from strong Cyp inhibition and were found to be metabolically unstable by incubation in human hepatocytes and microsomes. Installation of a pyrimary alcohol group on the heteroaryl ethyl group of the scaffold consistently improved Cyp3A4 liability, and led to improvement in physical and DMPK properties as well as improvement of their metabolic stability in human Heps. The lead compound from this series was orally administrated to SCID mice in a Del xenograft model and achieved greater than 90% phospho-ALK inhibition over 6 hours post dose at 10 mg/kg dose. The lead compound was subsequently tested against Crizotinib-resistant ALK mutations in enzyme assays, and was shown to inhibit the clinically relevant ALK mutations, including L1196M. In enzyme assays, it was inactive against G1269S mutation, consistent with modeling studies. Subsequent profiling in an FDCP cell line over expressing ALK G1269S mutation showed potent anti-proliferative activity, suggesting off-target activity. Further characterization of this series identified AurB inhibition to be a key cell cycle kinase responsible for the off-target activity in the engineered cell line. The off target activity hinders it from assessing the primary pharmacology responsible for its preclinical efficacy in disease relevant models. In conclusion, we have identified a novel orally bioavailable compound that is a potent dual active ALK and AurB inhibitor that is active against clinically-relevant gatekeeper mutant.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3910. doi:1538-7445.AM2012-3910

Discovery of (+)-N-(3-aminopropyl)-N-[1-(5-benzyl-3-methyl-4-oxo-[1,2]thiazolo[5,4-d]pyrimidin-6-yl)-2-methylpropyl]-4-methylbenzamide (AZD4877), a kinesin spindle protein inhibitor and potential anticancer agent

Structure-activity relationship analysis identified (+)-N-(3-aminopropyl)-N-[1-(5-benzyl-3-methyl-4-oxo-[1,2]thiazolo[5,4-d]pyrimidin-6-yl)-2-methylpropyl]-4-methylbenzamide (AZD4877), from a series of novel kinesin spindle protein (KSP) inhibitors, as exhibiting both excellent biochemical potency and pharmaceutical properties suitable for clinical development. The selected compound arrested cells in mitosis leading to the formation of the monopolar spindle phenotype characteristic of KSP inhibition and induction of cellular death. A favorable pharmacokinetic profile and notable in vivo efficacy supported the selection of this compound as a clinical candidate for the treatment of cancer.