Benzimidazoisoquinolines: a new class of rapidly metabolized aryl hydrocarbon receptor (AhR) ligands that induce AhR-dependent Tregs and prevent murine graft-versus-host disease

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that plays multiple roles in regulation of immune and inflammatory responses. The ability of certain AhR ligands to induce regulatory T cells (Tregs) has generated interest in developing AhR ligands for therapeutic treatment of immune-mediated diseases. To this end, we designed a screen for novel Treg-inducing compounds based on our understanding of the mechanisms of Treg induction by the well-characterized immunosuppressive AhR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We screened a ChemBridge small molecule library and identified 10-chloro-7H-benzimidazo[2,1-a]benzo[de]Iso-quinolin-7-one (10-Cl-BBQ) as a potent AhR ligand that was rapidly metabolized and not cytotoxic to proliferating T cells. Like TCDD,10-Cl-BBQ altered donor CD4⁺ T cell differentiation during the early stages of a graft versus host (GVH) response resulting in expression of high levels of CD25, CTLA-4 and ICOS, as well as several genes associated with Treg function. The Treg phenotype required AhR expression in the donor CD4⁺ T cells. Foxp3 was not expressed in the AhR-induced Tregs implicating AhR as an independent transcription factor for Treg induction. Structure-activity studies showed that unsubstituted BBQ as well as 4, 11-dichloro-BBQ were capable of inducing AhR-Tregs. Other substitutions reduced activation of AhR. Daily treatment with 10-Cl-BBQ during the GVH response prevented development of GVH disease in an AhR-dependent manner with no overt toxicity. Together, our data provide strong support for development of select BBQs that activate the AhR to induce Tregs for treatment of immune-mediated diseases.

Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer

PURPOSE

Patients with small-cell lung cancer (SCLC) have an exceptionally poor prognosis, calling for improved real-time noninvasive biomarkers of therapeutic response.

EXPERIMENTAL DESIGN

We performed targeted error-correction sequencing on 171 serial plasmas and matched white blood cell (WBC) DNA from 33 patients with metastatic SCLC who received treatment with chemotherapy (n = 16) or immunotherapy-containing (n = 17) regimens. Tumor-derived sequence alterations and plasma aneuploidy were evaluated serially and combined to assess changes in total cell-free tumor load (cfTL). Longitudinal dynamic changes in cfTL were monitored to determine circulating cell-free tumor DNA (ctDNA) molecular response during therapy.

RESULTS

Combined tiered analyses of tumor-derived sequence alterations and plasma aneuploidy allowed for the assessment of ctDNA molecular response in all patients. Patients classified as molecular responders (n = 9) displayed sustained elimination of cfTL to undetectable levels. For 14 patients, we observed initial molecular responses, followed by ctDNA recrudescence. A subset of patients (n = 10) displayed a clear pattern of molecular progression, with persistence of cfTL across all time points. Molecular responses captured the therapeutic effect and long-term clinical outcomes in a more accurate and rapid manner compared with radiographic imaging. Patients with sustained molecular responses had longer overall (log-rank P = 0.0006) and progression-free (log-rank P < 0.0001) survival, with molecular responses detected on average 4 weeks earlier than imaging.

CONCLUSIONS

ctDNA analyses provide a precise approach for the assessment of early on-therapy molecular responses and have important implications for the management of patients with SCLC, including the development of improved strategies for real-time tumor burden monitoring. See related commentary by Pellini and Chaudhuri, p. 2176.

11-Cl-BBQ, a select modulator of AhR-regulated transcription, suppresses lung cancer cell growth via activation of p53 and p27Kip1

Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor and functions as a tumour suppressor in different cancer models. In the present study, we report detailed characterization of 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ) as a select modulator of AhR-regulated transcription (SMAhRT) with anti-cancer actions. Treatment of lung cancer cells with 11-Cl-BBQ induced potent and sustained AhR-dependent anti-proliferative effects by promoting G1 phase cell cycle arrest. Investigation of 11-Cl-BBQ-induced transcription in H460 cells with or without the AhR expression by RNA-sequencing revealed activation of p53 signalling. In addition, 11-Cl-BBQ suppressed multiple pathways involved in DNA replication and increased expression of cyclin-dependent kinase inhibitors, including p27Kip1 , in an AhR-dependent manner. CRISPR/Cas9 knockout of individual genes revealed the requirement for both p53 and p27Kip1 for the AhR-mediated anti-proliferative effects. Our results identify 11-Cl-BBQ as a potential lung cancer therapeutic, highlight the feasibility of targeting AhR and provide important mechanistic insights into AhR-mediated-anticancer actions.

Circulating Tumor DNA as a Biomarker of Radiographic Tumor Burden in SCLC

Introduction

Blood-based next-generation sequencing assays of circulating tumor DNA (ctDNA) have the ability to detect tumor-associated mutations in patients with SCLC. We sought to characterize the relationship between ctDNA mean variant allele frequency (VAF) and radiographic total-body tumor volume (TV) in patients with SCLC.

Methods

We identified matched blood draws and computed tomography (CT) or positron emission tomography (PET) scans within a prospective SCLC blood banking cohort. We sequenced plasma using our previously developed 14-gene SCLC-specific ctDNA assay. Three-dimensional TV was determined from PET and CT scans using MIM software and reviewed by radiation oncologists. Univariate association and multivariate regression analyses were performed to evaluate the association between mean VAF and total-body TV.

Results

We analyzed 75 matched blood draws and CT or PET scans from 25 unique patients with SCLC. Univariate analysis revealed a positive association between mean VAF and total-body TV (Spearman’s ρ = 0.292, p < 0.01), and when considering only treatment-naive and pretreatment patients (n = 11), there was an increase in the magnitude of association (ρ = 0.618, p = 0.048). The relationship remained significant when adjusting for treatment status and bone metastases (p = 0.046). In the subgroup of patients with TP53 variants, univariate analysis revealed a significant association (ρ = 0.762, p = 0.037) only when considering treatment-naive and pretreatment patients (n = 8).

Conclusions

We observed a positive association between mean VAF and total-body TV in patients with SCLC, suggesting mean VAF may represent a dynamic biomarker of tumor burden that could be followed to monitor disease status.

Abstract B20: Prolonged time to clearance of circulating-tumor DNA from patients with limited-stage small-cell lung cancer is associated with inferior progression-free and overall survival

Introduction: Despite recent incremental advances, patients with small-cell lung cancer (SCLC) continue to have a poor prognosis, with a median overall survival (OS) of 12-20 months in limited-stage disease (LS-SCLC) and approximately 12 months in extensive-stage disease (ES-SCLC). In an attempt to improve the detection and monitoring of SCLC, assays of circulating tumor DNA (ctDNA) via blood-based next-generation sequencing (NGS) have been validated. In this study, we used a blood-based 14 gene SCLC ctDNA NGS panel to evaluate the prognostic significance of the diagnostic maximum ctDNA variant allele frequency (VAF), diagnostic mean ctDNA VAF, and time to ctDNA clearance while on first-line therapy.

Design: In our previous work, we developed a ctDNA assay to sequence 14 genes (TP53, RB1, BRAF, KIT, NOTCH1-4, PIK3CA, PTEN, FGFR1, MYC, MYCL1, and MYCN) that are commonly mutated in SCLC. A total of 104 plasma samples were analyzed from a cohort of 14 patients with LS-SCLC who completed definitive chemoradiation (n=13) or surgical resection (n=1) and had an end-of-treatment blood collection within nine weeks (mean 10.5 days, range 0-63 days) of completion of definitive initial therapy. We used a Cox Proportional Hazards model to estimate the hazard ratio (HR) for progression-free survival (PFS) or death based on the diagnostic maximum ctDNA VAF, diagnostic mean ctDNA VAF, and time to ctDNA clearance on first-line therapy.

Results: In our 14-patient cohort, we did not observe any association between progression or death and maximum diagnostic ctDNA VAF (PFS HR: 1.01, CI 0.97-1.05; OS HR: 1, CI 0.95-1.04) or mean diagnostic ctDNA VAF (PFS HR: 1.01, CI 0.94-1.08; OS HR: 0.99, CI 0.91-1.07). Of the specific mutations representing the maximum diagnostic ctDNA VAF, TP53 represented 14.2% (n=2), while the remaining included RB1 associated mutations (n=5), PIK3CA (n=1), MYCL1 amplification (n=1), or no ctDNA at diagnosis (n=5). Among patients with clearance of ctDNA during first-line therapy (n=9), delayed time to ctDNA clearance was associated with inferior PFS (HR 1.1, CI 1.01-1.19) and OS (HR 1.07, CI 1.01-1.15), with median time to clearance of 63 days (range 29-92 days). Notably, 3 patients cleared ctDNA on their first on-treatment draw at approximately 30 days (29, days, 29 days, and 32 days). These patients have had no evidence of relapse and all remain alive since the start of first-line treatment (1467, 965, and 383 days of follow-up). Of the patients who had disease recurrence, the median time to clearance on first-line therapy was 65 days and median time to progression was 249 days, with all but 1 patient succumbing to their disease (median OS 437 days).

Conclusion: In patients with LS-SCLC, prolonged time to ctDNA clearance during first-line therapy is associated with inferior PFS and OS. Larger patient cohorts are needed to validate this finding.

Citation Format: Christopher Cann, Prasad Kopparapu, Yingjun Yan, Anel Muterspaugh, Heidi Chen, Zhiguo Zhao, Sally York, Leora Horn, Kristen Ancell, Kenneth Wyman, Caterina Bertucci, Tristan Shaffer, Lauren Hodson, Kavita Garg, Seyed Ali Hosseini, Lee Lim, Christine M. Lovly, Wade Iams. Prolonged time to clearance of circulating-tumor DNA from patients with limited-stage small-cell lung cancer is associated with inferior progression-free and overall survival [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B20.

Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes

Small cell lung cancer (SCLC) is an aggressive malignancy composed of distinct transcriptional subtypes, but implementing subtyping in the clinic has remained challenging, particularly due to limited tissue availability. Given the known epigenetic regulation of critical SCLC transcriptional programs, we hypothesized that subtype-specific patterns of DNA methylation could be detected in tumor or blood from SCLC patients. Using genomic-wide reduced-representation bisulfite sequencing (RRBS) in two cohorts totaling 179 SCLC patients and using machine learning approaches, we report a highly accurate DNA methylation-based classifier (SCLC-DMC) that can distinguish SCLC subtypes. We further adjust the classifier for circulating-free DNA (cfDNA) to subtype SCLC from plasma. Using the cfDNA classifier (cfDMC), we demonstrate that SCLC phenotypes can evolve during disease progression, highlighting the need for longitudinal tracking of SCLC during clinical treatment. These data establish that tumor and cfDNA methylation can be used to identify SCLC subtypes and might guide precision SCLC therapy.

Abstract 715: Circulating tumor DNA as a potential biomarker of radiographic tumor burden in small cell lung cancer

Introduction

Blood-based next generation sequencing assays of circulating tumor DNA (ctDNA) have the ability to detect canonical SCLC tumor-associated mutations1,2. In non-small cell lung cancer, mean variant allele frequency (VAF) of clonal mutations in ctDNA is associated with radiographic tumor volume (TV)3. We sought to characterize the relationship between ctDNA mean VAF and total-body tumor burden in patients with SCLC.

Methods

Patients with both limited- and extensive-stage SCLC were identified prospectively and underwent serial blood draws as part of an IRB-approved protocol (IRB #030763). Using our previously developed ctDNA assay, mean VAF was calculated from patient plasma by sequencing 14 genes (all coding exons of TP53, RB1, BRAF, KIT, NOTCH1-4, PIK3CA, PTEN, and copy number variations in FGFR1, MYC, MYCL1, and MYCN)1,4. Three-dimensional total-body tumor burden was determined from positron emission tomography and computed tomography scans obtained during routine care using a radiation oncology treatment-planning software (MIM), and tumor segmentations were verified by radiation oncologists. Univariate association and multivariable mixed effects regression analyses (including presence of bone metastases and treatment status) were performed to evaluate the association between mean VAF and overall TV. We performed separate analyses for mean VAF of all variants identified and of TP53 variants only.

Results

We analyzed 75 concordant scans and blood draws from 25 patients with SCLC. The median interval between imaging and blood collection was 1 day (mean 3.5, range 0-16).

Univariate analysis showed a positive association between mean VAF of all variants and overall TV (Spearman's ρ=0.292, p&lt;0.01). When considering only treatment-naïve and pre-treatment samples (n=11), the magnitude of association increased and remained significant (ρ=0.618, p=0.048). The relationship between mean VAF of all variants and overall TV remained significant when adjusting for treatment status and bone metastases (p=0.046). When considering only TP53 variants, an overall univariate correlation analysis did not show a significant association between mean VAF and overall TV (ρ=0.184, p=0.175). However, among treatment-naïve and pre-treatment samples (n=8) with TP53 variants, the association was significant (ρ=0.762, p=0.037). This association remained significant (p=0.021) after adjusting for treatment status and presence of bone metastasis, with VAF increasing 3.7% for each fold increase in TV (95% CI: 0.7-6.7%).

Conclusion

In our study mean VAF (both overall and TP53 variants only) was positively correlated with three-dimensional total-body tumor burden in patients with SCLC. These results suggest that mean VAF may provide a useful snapshot of overall tumor burden and represent a dynamic biomarker that could be followed to monitor for disease progression in patients with SCLC.

References 1. Almodovar K, et al. Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer... J Thorac Oncol 2018;13:112-23. 2. Nong J, et al. ctDNA analysis depicts subclonal architecture...of small cell lung cancer. Nat Commun 2018;9:3114. 3. Abbosh C, et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017;545:446-51. 4. George J, et al. Comprehensive genomic profiles of small cell lung cancer. Nature 2015;524:47.

Citation Format: Jarrod T. Smith, Aneri Balar, Dhairya A. Lakhani, Christien Kluwe, Zhiguo Zhao, Prasad Kopparapu, Karinna Almodovar, Anel Muterspaugh, Yingjun Yan, Sally York, Leora Horn, Sanja Antic, Caterina Bertucci, Tristan Shaffer, Lauren Hodsdon, Kavita Garg, Seyed Ali Hosseini, Lee Lim, Evan Osmundson, Pierre Massion, Christine Lovly, Wade Iams. Circulating tumor DNA as a potential biomarker of radiographic tumor burden in small cell lung cancer [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 715.

Abstract P3-06-04: Bcl-2 functional converters inhibit tumor growth and metastatic potential in zebrafish xenografts

While potential therapies might have pronounced success in the simplified settings in cell culture medium, many drugs fail or underperform when cancer cells are encased in a complex 3D microenvironment. Although, rat and mouse models will continue to be the gold standard for in vivo data in drug discovery, zebrafish xenograft models have emerged as a powerful model that can quickly and efficiently deliver in vivo drug efficacy data before commitment to expensive and time consuming rodent models. We have discovered several compounds that work as B-cell lymphoma 2 (Bcl-2) functional converters and activate Bcl-2 into a killer instead of its native anti-apoptotic role. In this study, we use a zebrafish xenograft model to evaluate the ability of these compounds to inhibit xenograft tumor growth of Bcl-2 expressing cancer cells, including triple negative breast cancers. Live fluorescent imaging of cancer cells within zebrafish embryos revealed a decrease in cancer cell growth while under treatment of compounds. Furthermore, the agents that converted Bcl-2 into pro-apoptotic protein also inhibited the metastatic potential of the cancer cells. Therefore, this study demonstrates zebrafish xenograft techniques that can be used to quickly and efficiently obtain in vivo drug discovery data. Moreover, we report novel Bcl-2 functional converter compounds that can effectively reduce xenograft tumor growth and its ability to invade tissue in a living 3D environment and establish the role of Bcl-2 in cancer progression.

Citation Format: Gamble J, Pearce M, Kopparapu P, Jang HS, Tanguay R, Greenwood J, Kolluri S. Bcl-2 functional converters inhibit tumor growth and metastatic potential in zebrafish xenografts [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-06-04.