Nonpathogenic E. coli engineered to surface display cytokines as a new platform for immunotherapy

Given the safety, tumor tropism, and ease of genetic manipulation in non-pathogenic Escherichia coli (E. coli), we designed a novel approach to deliver biologics to overcome poor trafficking and exhaustion of immune cells in the tumor microenvironment, via the surface display of key immune-activating cytokines on the outer membrane of E. coli K-12 DH5α. Bacteria expressing murine decoy-resistant IL18 mutein (DR18) induced robust CD8+ T and NK cell-dependent immune responses leading to dramatic tumor control, extending survival, and curing a significant proportion of immune-competent mice with colorectal carcinoma and melanoma. The engineered bacteria demonstrated tumor tropism, while the abscopal and recall responses suggested epitope spreading and induction of immunologic memory. E. coli K-12 DH5α engineered to display human DR18 potently activated mesothelin-targeting CAR NK cells and safely enhanced their trafficking into the tumors, leading to improved control and survival in xenograft mice bearing mesothelioma tumor cells, otherwise resistant to NK cells. Gene expression analysis of the bacteria-primed CAR NK cells showed enhanced TNFα signaling via NFkB and upregulation of multiple activation markers. Our novel live bacteria-based immunotherapeutic platform safely and effectively induces potent anti-tumor responses in otherwise hard-to-treat solid tumors, motivating further evaluation of this approach in the clinic.

Patient-Specific Vascularized Tumor Model: Blocking TAM Recruitment with Multispecific Antibodies Targeting CCR2 and CSF-1R

Tumor-associated inflammation drives cancer progression and therapy resistance, with the infiltration of monocyte-derived tumor-associated macrophages (TAMs) associated with poor prognosis in diverse cancers. Targeting TAMs holds potential against solid tumors, but effective immunotherapies require testing on immunocompetent human models prior to clinical trials. Here, we develop an in vitro model of microvascular networks that incorporates tumor spheroids or patient tissues. By perfusing the vasculature with human monocytes, we investigate monocyte trafficking into the tumor and evaluate immunotherapies targeting the human tumor microenvironment. Our findings demonstrate that macrophages in vascularized breast and lung tumor models can enhance monocyte recruitment via TAM-produced CCL7 and CCL2, mediated by CSF-1R. Additionally, we assess a novel multispecific antibody targeting CCR2, CSF-1R, and neutralizing TGF-β, referred to as CSF1R/CCR2/TGF-β Ab, on monocytes and macrophages using our 3D models. This antibody repolarizes TAMs towards an anti-tumoral M1-like phenotype, reduces monocyte chemoattractant protein secretion, and effectively blocks monocyte migration. Finally, we show that the CSF1R/CCR2/TGF-β Ab inhibits monocyte recruitment in patient-specific vascularized tumor models. Overall, this vascularized tumor model offers valuable insights into monocyte recruitment and enables functional testing of innovative therapeutic antibodies targeting TAMs in the tumor microenvironment (TME).

Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer

Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor-positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated β2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell-mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer.

SIGNIFICANCE

Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.

Abstract 2181: Genomic correlates of Metastasis in KRAS mutant lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) is a disease classified by molecular markers. In KRAS-mutant LUAD, STK11 and KEAP1 mutations are associated with decreased overall survival (OS), but predictors of metastasis have been poorly defined. In this study, we identify clinical and genomic predictors of metastatic KRAS-mutant LUAD.

Methods: Patients with KRAS-mutant LUAD profiled by targeted next generation sequencing (OncoPanel) were included. Stage, histology, recurrence-free and overall survival were assessed. Clinical and genomic features between metastatic vs non-metastatic samples were compared. KRAS-mutant LUAD samples profiled using MSK-IMPACT in the AACR GENIE database were used to validate our findings. Continuous variables were compared using the Mann-Whitney U test and categorical variables were compared using the Fisher’s Exact test. Survival analysis was performed using the Cox Proportional Hazards model. WExT was used to identify co-occurring and mutually exclusive genetic alterations. Benjamini-Hochberg was used to correct for multiple comparisons. P-values < 0.05 and q-values < 0.10 were considered significant.

Results: In the OncoPanel cohort (metastatic n=290; non-metastatic n=324), tumor mutational burden (TMB) (p = .001) and KEAP1 mutations (q = 0.05) were enriched in metastatic samples, while NFKBIA amplifications (q = 0.07) were enriched in non-metastatic samples. KEAP1/STK11 mutations significantly co-occurred (q < 1e-8). Compared to double wild-type samples: KEAP1/STK11 co-mutations were significantly enriched in metastatic samples (n = 72, p = 0.0002, OR 3.4); KEAP1-mutant samples trended towards enrichment in metastatic samples, (n = 21,p = 0.07, OR 2.47); STK11 mutations did not associate with stage (n = 53, p = 0.88, OR = 0.94). In multivariable survival analysis, metastasis (p < 0.005), KEAP1 mutation (p=0.01), and STK11 mutation (p=0.02) were associated with worse OS.

In the MSK-IMPACT validation cohort (metastatic site n=417, primary site n = 781), KEAP1 was the only gene enriched in metastatic samples (q < 0.001) at q < 0.05. Compared to double wild type samples: KEAP/STK11 co-mutations (n=138, p < 0.0001, OR 2.1) and KEAP1 mutations (n=59, p = 0.04, OR 1.77) were enriched in metastatic samples; STK11-mutations did not associate with metastasis (n = 190, p = 0.34, OR 0.83). Other predictors of metastasis included Fraction Genome Altered (FGA) (p < 1e-5), TMB (p < 1e-5), and CDKN2A/B deletions (q < 0.003).

Conclusion: While both KEAP1 and STK11 mutations are associated with decreased OS in KRAS-mutant LUAD, we find in two independent cohorts that only KEAP1 mutations and KEAP1/STK11 co-mutations, but not STK11 mutations, are associated with metastasis. We also found that FGA, TMB, CDKN2A/B deletions are strongly associated with metastasis. Further research is necessary to understand the influence of KEAP1 mutations, independent of and in-conjunction with STK11 mutations, on metastasis.

Citation Format: Daniel Boiarsky, Christine A. Lydon, Emily Chambers, Pasi A. Janne, Mark M. Awad, Eliezer M. Van Allen, David Barbie, Natalie I. Vokes. Genomic correlates of Metastasis in KRAS mutant lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2181.

Diminished Efficacy of Programmed Death-(Ligand)1 Inhibition in STK11- and KEAP1-Mutant Lung Adenocarcinoma Is Affected by KRAS Mutation Status

INTRODUCTION

STK11 and KEAP1 mutations (STK11 mutant [STK11MUT] and KEAP1MUT) are among the most often mutated genes in lung adenocarcinoma (LUAD). Although STK11MUT has been associated with resistance to programmed death-(ligand)1 (PD-[L]1) inhibition in KRASMUT LUAD, its impact on immunotherapy efficacy in KRAS wild-type (KRASWT) LUAD is currently unknown. Whether KEAP1MUT differentially affects outcomes to PD-(L)1 inhibition in KRASMUT and KRASWT LUAD is also unknown.

METHODS

Clinicopathologic and genomic data were collected from September 2013 to September 2020 from patients with advanced LUAD at the Dana-Farber Cancer Institute/Massachusetts General Hospital cohort and the Memorial Sloan Kettering Cancer Center/MD Anderson Cancer Center cohort. Clinical outcomes to PD-(L)1 inhibition were analyzed according to KRAS, STK11, and KEAP1 mutation status in two independent cohorts. The Cancer Genome Atlas transcriptomic data were interrogated to identify differences in tumor gene expression and tumor immune cell subsets, respectively, according to KRAS/STK11 and KRAS/KEAP1 comutation status.

RESULTS

In the combined cohort (Dana-Farber Cancer Institute/Massachusetts General Hospital + Memorial Sloan Kettering Cancer Center/MD Anderson Cancer Center) of 1261 patients (median age = 61 y [range: 22-92], 708 women [56.1%], 1065 smokers [84.4%]), KRAS mutations were detected in 536 cases (42.5%), and deleterious STK11 and KEAP1 mutations were found in 20.6% (260 of 1261) and 19.2% (231 of 1202) of assessable cases, respectively. In each independent cohort and in the combined cohort, STK11 and KEAP1 mutations were associated with significantly worse progression-free (STK11 hazard ratio [HR] = 2.04, p < 0.0001; KEAP1 HR = 2.05, p < 0.0001) and overall (STK11 HR = 2.09, p < 0.0001; KEAP1 HR = 2.24, p < 0.0001) survival to immunotherapy uniquely among KRASMUT but not KRASWT LUADs. Gene expression ontology and immune cell enrichment analyses revealed that the presence of STK11 or KEAP1 mutations results in distinct immunophenotypes in KRASMUT, but not in KRASWT, lung cancers.

CONCLUSIONS

STK11 and KEAP1 mutations confer worse outcomes to immunotherapy among patients with KRASMUT but not among KRASWT LUAD. Tumors harboring concurrent KRAS/STK11 and KRAS/KEAP1 mutations display distinct immune profiles in terms of gene expression and immune cell infiltration.

EXTH-81. STING ACTIVATION PROMOTES ROBUST IMMUNE RESPONSE AND TUMOR REGRESSION IN GLIOBLASTOMA MODELS

The immunosuppressive tumor microenvironment in glioblastoma presents a major barrier to effective application of immunotherapeutic approaches in this disease. Although immunotherapy has had a tremendous impact on cancer treatment in the past decade, with hitherto unseen responses at advanced and metastatic stages of the disease glioblastoma remains largely refractory to current immunotherapeutic approaches. The cGAS-STING cytoplasmic double stranded DNA sensing pathway has emerged as a next-generation immunotherapy target with potent local immune stimulatory properties, but has not been well investigated in glioblastoma to date. Here we investigated the presence of STING pathway components in glioblastoma patient specimens and cell lines by Western blotting and immunostaining. The functionality of the pathway was determined by ELISA, and immune infiltrates, and animal survival were investigated in mouse glioblastoma models after treatment with the STING agonist ADU-S100. Our data reveal the presence of STING in human GBM specimens, where it stains strongly in the tumor vasculature, and appears to be activated as evidenced by elevated phosphoTBK1 staining. We show that human GBM cells do not respond agonists, but that GBM explants can respond to STING agonist treatment by secretion of inflammatory cytokines. In murine GBM models, we show a profound shift in the tumor immune landscape after STING agonist treatment, with massive infiltration of the tumor-bearing hemisphere with innate immune cells including inflammatory macrophages, neutrophils and NK populations. Treatment of established murine intracranial GL261 and CT-2A tumors by biodegradable ADU-S100-loaded intracranial implants demonstrated a significant increase in survival in both models and long-term survival with immune memory in GL261. This study reveals therapeutic potential and deep remodeling of the TME by STING activation in GBM and warrants the further examination of STING agonists alone or in combination with other immunotherapies such as cancer vaccines, CAR T cells, or immune checkpoint blockade.

Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer

Clinical trial results have recently demonstrated that inhibiting inflammation by targeting the interleukin-1β pathway can offer a significant reduction in lung cancer incidence and mortality, highlighting a pressing and unmet need to understand the benefits of inflammation-focused lung cancer therapies at the genetic level. While numerous genome-wide association studies (GWAS) have explored the genetic etiology of lung cancer, there remains a large gap between the type of information that may be gleaned from an association study and the depth of understanding necessary to explain and drive translational findings. Thus, in this study we jointly model and integrate extensive multiomics data sources, utilizing a total of 40 genome-wide functional annotations that augment previously published results from the International Lung Cancer Consortium (ILCCO) GWAS, to prioritize and characterize single nucleotide polymorphisms (SNPs) that increase risk of squamous cell lung cancer through the inflammatory and immune responses. Our work bridges the gap between correlative analysis and translational follow-up research, refining GWAS association measures in an interpretable and systematic manner. In particular, reanalysis of the ILCCO data highlights the impact of highly associated SNPs from nuclear factor-κB signaling pathway genes as well as major histocompatibility complex mediated variation in immune responses. One consequence of prioritizing likely functional SNPs is the pruning of variants that might be selected for follow-up work by over an order of magnitude, from potentially tens of thousands to hundreds. The strategies we introduce provide informative and interpretable approaches for incorporating extensive genome-wide annotation data in analysis of genetic association studies.

Abstract 5543: TAK1 deficiency in tumor cells enhances sensitivity to CTL-mediated killing via TNF-α

The clinical successes achieved by different immunotherapies have resulted in a paradigm shift in treatment modalities. Despite these significant advances, not all patients benefit from the use of these therapies, creating a need to develop additional approaches to enhance and broaden their clinical application. To identify genes whose products can increase or decrease the sensitivity of tumor cells to the immune system, we used a CTL assay to screen a whole genomic CRISPR library. We co-culture a mouse cell line, ID8, expressing a model antigen (Ova) with transgenic CD8 T cells (OT-I) recognizing this antigen. A set of controls that enhance or decrease CTL activity behaved as expected. Comparison of the CRISPR score identified several hits that increased or decreased the sensitivity of the tumor cells to CTL killing. Subsets of these hits belong to two pathways involved in CTL-mediated killing: the IFN-γ and the TNF-α signaling pathways. We evaluated which of these hits would be amenable to therapeutic modulation, and decided to focus on the kinase TAK1 for confirmation and validation studies. A TAK1 deficient cell line was more sensitive to CTL killing, which was prevented by expression of TAK1, confirming the role of TAK1 in this process. A TAK1 gene carrying an inactivation mutation K63W did not rescue the effects of TAK1 KO, indicating that TAK1 enzymatic activity was necessary. Several pathways mediate CTL killing: Perforin/Granzyme B, IFN-γ, TNF-α, Fas & TRAIL pathways. To determine TAK1 MOA, we studied the effects of a Perforin/Granzyme B inhibitor CMA. CMA inhibited CTL activity in a dose-dependent manner on WT cells, but did not inhibit CTL activity on TAK1 deficient cells, indicating TAK1 effects are independent of this pathway. We then tested the sensitivity of TAK1 KO cells to TNF-α. TAK1 KO cells were more sensitive to TNF-α mediated killing, and similar results were observed with several additional cell lines (MC38, EMT6, KP). TNF-α can activate the JNK, p38, and NF-κB pathways, and the apoptosis extrinsic pathway to regulate cell growth and cell death. Kinetics studies monitoring pathway activity upon TNF-α stimulation showed that TAK1 KO cell lines induced cFLIP degradation before observing PARP cleavage, and that the NF-κB pathway, which has been observed to mediate cFLIP synthesis, was not activated. We proceeded to evaluate the effects of TAK1 deficiency in a mouse syngeneic model. TAK1 deficiency resulted in reduced growth and increased survival in the MC38 in vivo model. In summary, by screening a CRISPR library against a CTL assay, we identified TAK1 as a novel potential target for immunotherapies. TAK1 deficiency enhances CTL killing and results in decreased tumor growth and increased survival in vivo. This results support the development of TAK1 inhibitors to enhance the anti-tumor action of the immune system.

Citation Format: Juan J. Miret, Troy A. Luster, Patrick Lizotte, Min Wu, Sarah Nzikoba, Luke Taus J. Taus, Prafulla C. Gokhale, Paul Kirschmeier, David Barbie, Cloud P. Paweletz. TAK1 deficiency in tumor cells enhances sensitivity to CTL-mediated killing via TNF-α [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 5543.

Abstract 1483: Ex vivo single cell RNA-sequencing of tumor derived organotypic spheroids identifies a unique mesenchymal resistance program to PD-1 blockade

Introduction: Immune checkpoint blockade, including αPD-1 and αPD-L1 form the backbone of personalized medicine for lung cancer and other malignancies. Yet the underlying mechanisms of resistance to therapy are not fully characterized partly because functional models to perform mechanistic studies are lacking. Here we report on single cell RNA sequencing from murine (or patient) derived organotypic tumor spheroids (DOTS-seq) that enables analysis of tumor and immune cell intrinsic changes that occur during αPD-1 treatment ex vivo.

Methods: Murine-derived organotypic spheroids from syngeneic MC38 tumors were grown and treated with αPD-1 and isotype matched IgG in a microfluidic device as previously described1. At day 6, libraries were prepared from individual viable cells using the 10X Genomics platform and sequenced at DFCI. Sequencing data was processed using the Seurat package and corrected for UMI, ribosomal, mitochondrial and cell cycle transcripts. Dimensionality reduction, clustering, and identification of differentially expressed genes were performed on log normalized data. Gene set enrichment analysis was performed using the SetRank package.

Results: Transcripts were obtained for 2,543 IgG treated and 2,626 αPD-1 treated cells that were resistant to ex vivo killing. 60% of αPD-1 treated cells fell into 2 unique clusters which each had downregulated genes associated with apoptosis and interferon-γ response, such as Dap, Cxcl10 and B2m. Within these two, one cluster contained highly upregulated genes known to be E2F targets or important for G2M transition while the other did not. Interestingly, the quiescent subpopulation exhibited a unique epithelial to mesenchymal transition-like state characterized by expression of Snai1, Mmp2, Mmp14, and Vegfa. This subpopulation also upregulated transcripts of immuno-modulatory cytokines from the IL6 family, including Il11, Lif, and Osm. IL-6 extracellular levels are also elevated in treated cultures, suggesting a mesenchymal-like cell subpopulation responsible for this cytokine modulation of the tumor microenvironment.

Conclusion: Here we show that profiling the interplay between tumor and immune cells at the single cell level is possible ex vivo. We identify a previously uncharacterized subpopulation of EMT-like cells that regulate the tumor microenvironment and promote resistance to αPD-1 in MC38 tumors.

Reference: 1. Jenkins RW, et al. Cancer Discov DOI:10.1158/2159-8290

Citation Format: Andrew J. Portell, Jonathan Greene, Luke J. Taus, Patrick Lizotte, Elena Ivanova, Kalil O. Menezes, Amir R. Aref, Paul Kirschmeier, Russell W. Jenkins, David Barbie, Cloud P. Paweletz. Ex vivo single cell RNA-sequencing of tumor derived organotypic spheroids identifies a unique mesenchymal resistance program to PD-1 blockade [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 1483.

Phase 1 dose-escalation study of momelotinib, a Janus kinase 1/2 inhibitor, combined with gemcitabine and nab-paclitaxel in patients with previously untreated metastatic pancreatic ductal adenocarcinoma

Purpose Preclinical evidence suggests the importance of Janus activating kinase (JAK) and TANK-binding kinase 1 (TBK1) in pancreatic ductal adenocarcinoma (PDAC). We evaluated the safety and efficacy of momelotinib (MMB), a JAK1/2 inhibitor with additional activity against TBK1, plus albumin-bound paclitaxel + gemcitabine (nab-P + G), in patients with previously untreated metastatic PDAC. Experimental Design Patients were enrolled into five cohorts of increasing doses of MMB between 100 and 200 mg administered once or twice daily in combination with nab-P + G in 28-day cycles to determine maximum tolerated dose (MTD). Safety, efficacy, pharmacokinetics, and pharmacodynamics were assessed for all patients. Results Twenty-five patients were enrolled. Dose-limiting toxicities of Grade 3 diarrhea occurred in 1 patient each in the 100 and 200 mg MMB once-daily dose groups. MTD was not reached. The 200 mg MMB twice-daily was the maximum administered dose. Objective response rate was 28% (all partial responses), and 13 (52%) patients had a best response of stable disease. The most common adverse events (AEs) were fatigue (80%), nausea (76%), and anemia (68%). Grade 3 or 4 AEs, most commonly neutropenia (32%), were reported by 88% of patients, of which 44% were considered related to MMB. Pharmacokinetic analyses showed MMB concentrations were too low for TBK1 inhibition. Conclusions MMB was safe and well tolerated in combination with nab-P + G. As no OS or PFS benefit vs nab-P + G was apparent in context of suboptimal engagement of the target TBK1, this study does not support further development of MMB as a first-line therapy in pancreatic cancer.

Abstract 3682: Synergistic immunostimulatory effects and therapeutic benefit of combined histone deacetylase and bromodomain inhibition in non-small cell lung cancer

Effective therapies for non-small cell lung cancer (NSCLC) remain challenging despite an increasingly comprehensive understanding of somatically altered oncogenic pathways. It is now clear that therapeutic agents with potential to impact the tumor immune microenvironment potentiate immune-orchestrated therapeutic benefit. This study evaluated the immunoregulatory properties of two classes of drugs that modulate the epigenome, histone deacetylase (HDAC) and bromodomain inhibitors with a focus on key cell subsets that are engaged in an immune response. By evaluating human peripheral blood and NSCLC tumors, we show that the selective HDAC6 inhibitor ricolinostat promotes phenotypic changes associated with enhanced T-cell priming and function of antigen presenting cells. The bromodomain inhibitor JQ1 attenuated CD4+Foxp3+ T regulatory cell suppressive function and synergized with ricolinostat to facilitate immune-mediated tumor growth arrest, leading to prolonged survival of mice with lung adenocarcinomas. Collectively, our findings highlight immunomodulatory effects of two epigenetic modifiers that together promote T-cell-mediated anti-tumor immunity and demonstrate their therapeutic potential for NSCLC treatment.

Citation Format: Dennis O. Adeegbe, Yan Liu, Patrick Lizotte, Yusuke Kamihara, Mark Awad, David Barbie, Jerome Ritz, Simon Jones, Steven Quayle, Peter Hammerman, Kwok-Kin Wong. Synergistic immunostimulatory effects and therapeutic benefit of combined histone deacetylase and bromodomain inhibition in non-small cell lung cancer [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 3682. doi:10.1158/1538-7445.AM2017-3682

Abstract LB-218: Validation of a novel microfluidic device for screening of immune checkpoint inhibitors using 3D organotypic tumor spheroids

Immune checkpoint blockade, including anti-PD-1 and PD-L1 therapies, is revolutionizing cancer care for melanoma, lung and other malignancies. However, pre-clinical models in which to rapidly and robustly evaluate the efficacy of these treatment approaches, including the development of combination therapies and/or relevant biomarkers, are lacking. We have developed a novel approach for evaluating ex vivo response to immune checkpoint blockade using murine- and patient derived organotypic tumor spheroids (mDOTS/pDOTS) cultured in a new 3D microfluidic system. We have demonstrated that spheroids isolated from fresh mouse and human tumor samples retain autologous lymphoid and myeloid cell populations.

Methods: Using MC38 and B16F10 syngeneic mouse cancer models with reported responsiveness or resistance to PD-1 blockade respectively, we treated mDOTS in the 3D microfluidic device with either control IgG or increasing concentrations of anti-PD-1 for up to 6 days and quantified cell viability by dual labeling fluorescence microscopy. To confirm tumor cell-specific death and survival of mDOTS immune component we applied multi-color immunofluorescent staining of CD8 as well as CD11b+ and CD11c+ myeloid cells in parallel with viability dye calcein AM. Tumor cell-specific death was assessed by absence of calcein AM and pyknotic nuclear staining in CD45 negative mDOTS component.

Results: We demonstrated dose-dependent killing following treatment with anti-PD-1 in MC38 spheroids. We showed presence of viable cytotoxic lymphocytes as well as other immune cells for up to 5 days of ex vivo growth, when we observed the beginning of tumor but not immune cell killing. In contrast, mDOTS derived from B16F10 melanoma, which is reported to be minimally sensitive to single agent PD-1 blockade, exhibited little cell death despite identical treatment and comparable immune profiles (at highest anti-PD-1 dose of 10ug/mL viability was 98.2%+0.04 versus 29.7%+1.68 in MC38) . No significant cell death (viability 88.2%+2.18) was also noted in spheroids generated from MC38 cell line alone, conceivably due to the absence of autologous cytotoxic T cells. Additional analysis of immune dynamics will be discussed.

Conclusions: These data demonstrate the ability to recapitulate sensitivity and innate resistance to PD-1 blockade ex vivo. By being able to study the impact of immunotherapy and targeted therapy in a rapid ex vivo system the development of drug combinations and their associated biomarkers can be significantly enhanced. The preclinical studies can be used to develop and guide the next generation clinical trials for lung cancer patients, and hopefully improving their success rate.

Citation Format: Elena Ivanova, Amir Aref, Russel Jenkins, Patrick Lizotte, Wei Huang, Sangeetha Palakurthi, Paul Kirschmeier, David Barbie, Cloud Paweletz, Pasi Janne, Kwok-Kin Wong. Validation of a novel microfluidic device for screening of immune checkpoint inhibitors using 3D organotypic tumor spheroids [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-218. doi:10.1158/1538-7445.AM2017-LB-218

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine.

Abstract A23: An integrated platform for the functional annotation of the cancer genome

The systematic characterization of mutations in cancer genomes through efforts such as The Cancer Genome Atlas will lead to a comprehensive list of alterations associated with particular cancers. A powerful complementary approach is to comprehensively characterize the functional basis of cancer, by identifying the genes essential for growth and related phenotypes in different cancer cells. Such information would be particularly valuable for identifying potential drug targets. The recent development of an efficient, robust approach to perform genome-scale pooled shRNA screens now permits the highly parallel identification of essential genes in cancer cells in a cost-effective manner. We have initiated a project to identify essential genes in 300 cancer cell lines representing a diverse range of lineages and genotypes. In each screen the abundance of 55,000 shRNA constructs targeting 11,000 genes is monitored in quadruplicate at the completion of 16 population doublings via hybridization of half-hairpin barcodes to a custom Affymetrix microarray. We have developed multiple complementary approaches for the analysis of this screening data at the shRNA level and at the gene level. shRNA level analytical tools include signal to noise and fold depletion metrics to identify individual shRNA constructs whose abundance at the completion of the experiment discriminates two classes of cell lines (e.g., KRASmut vs. KRASwt). Gene level analytical tools include RIGER, a gene-set enrichment analysis (GSEA)-based non-parametric algorithm which treats the 5 shRNA constructs targeting a given gene as a set and assesses bias of each gene-shRNA set as showing evidence of depletion during the experiment. Using these tools, we have begun to systematically identify known and novel anti-cancer drug targets via the integration of these functional screening results with corresponding structural cancer genomic data derived from both the screened cell lines and from known alterations in tumor samples. To facilitate this analysis, each of the screened cell lines has undergone comprehensive molecular characterization (DNA copy number, RNA expression, OncoMap high-throughput mutation profiling) to identify the genomic alterations harbored in its genome. Our preliminary data suggests that this integrated approach is efficient at pinpointing molecular targets that not only include genes altered in cancer genomes but additionally include genes exhibiting a synthetic lethal relationship with an oncogenic driver mutation (e.g., KRAS).We are validating candidate molecular targets using both loss-of-function and gain-of-function secondary screens. To facilitate these gain-of-function screens, we are creating a library of human open reading frames (ORFs) by sequencing and transferring the Human ORFeome collection, developed by the Center for Cancer Systems Biology at the Dana-Farber Cancer Institute, from Gateway Entry vectors into lentiviral expression vectors. This integrated platform for the unbiased, systematic functional annotation of the cancer genome represents an opportunity to identify molecular targets at genome-scale.

Citation Information: Cancer Res 2009;69(23 Suppl):A23.

Mullerian inhibiting substance inhibits ovarian cell growth through an Rb-independent mechanism

Müllerian inhibiting substance (MIS), a transforming growth factor-beta family member, causes regression of the Müllerian duct in male embryos. MIS overexpression in transgenic mice ablates the ovary, and MIS inhibits the growth of ovarian cancer cell lines in vitro, suggesting a key role for this hormone in postnatal development of the ovary. This report describes a mechanism for MIS-mediated growth inhibition in both a human epithelial ovarian cancer cell line and a cell line derived from normal ovarian surface epithelium, which is the origin of human epithelial ovarian cancers. MIS-treated cells accumulated in the G(1) phase of the cell cycle and subsequently underwent apoptosis. MIS up-regulated the cyclin-dependent kinase inhibitor p16 through an MIS type II receptor-mediated mechanism and inhibited growth in the absence of detectable or inactive Rb protein. Prolonged treatment with MIS down-regulated the Rb-related protein p130 and increased the Rb family-regulated transcription factor E2F1, overexpression of which inhibited growth. These findings demonstrate that p16 is required for MIS-mediated growth inhibition in ovarian epithelial cells and tumor cells and suggest that up-regulation of E2F1 also plays a role in this process.