Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity

Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic.

SIGNIFICANCE

This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.

Abstract 6377: A translatable tumor-killing platform with robust sensitivity towards immune checkpoint inhibitor targeted therapeutics

The cancer treatment landscape has transformed following the clinical success of early immune checkpoint inhibitors (ICI) which demonstrate the remarkable power of harnessing the immune system to treat a variety of metastatic cancers. Despite the success of Pembrolizumab, Nivolumab and Atezolizumab, the programmed cell death protein-1 (PD1)-programmed death ligand-1/2 (PD-L1/L2) pathway remains a tractable target for many drug discovery programs, particularly for bi-specific or combinational therapies. The PD1 - PD-L1/L2 pathway is important in protecting the host from uncontrolled immune responses, but can be hijacked by tumors, rendering them resistant to immune attack. Antibodies which antagonize this pathway potentiate T-cell mediated tumor destruction yet do not show efficacy in all patients or guarantee long-term protection, in part due to tumor-associated ICI-resistance mechanisms. There is a distinct need to develop novel ICI therapeutics and robust, complex co-culture platforms to better predict clinical efficacy. Here we outline a series of translationally relevant co-culture assays using Pembrolizumab as a benchmark therapeutic alongside other ICI. PD-1 expression levels are known to be low on resting T cells, as indeed are many checkpoint receptors, and so to enhance the therapeutic window, CD3+T cells from healthy human donors were polyclonally stimulated before addition to SK-OV-3 target cell cultures. The SK-OV-3 tumor line was stably transduced with NucLight Red (NLR) to allow co-localization of the caspase 3/7 signal to tumor cells. Autologous, mature monocyte-derived dendritic cells (moDC), expressing high levels of PD-L1/PD-L2 were added into tri-cultures in a 2D tumor killing assay. Tumor killing kinetics were quantified via live cell imaging using an Incucyte S3. Although Pembrolizumab enhanced immune-mediated direct (pre-stimulated) T cell killing, the therapeutic window increased in the presence of autologous moDC. Using a modified 3D (tumor spheroid) format over a longer time course, Pembrolizumab was also shown to enhance PBMC-mediated killing and the ability of moDC to enhance this effect further was determined. In recent years, the development and implementation of combinatorial approaches has resulted in significant improvements in patient responsiveness and disease outcomes for various cancers. Here, we describe a suite of tumor killing assays which can be adapted to multiple tumor or therapeutic targets, with a focus on immune involvement. ICI are shown to work robustly and efficacy tracks expression of the relevant checkpoint receptors, making this a powerful format in which to test combination therapies or novel ICI.

Citation Format: Marie Carkill, Kaitlin Mitchell, Lauren Kelsey, Jezrom Self-Fordham, Nunan Robert, Louise Brackenbury. A translatable tumor-killing platform with robust sensitivity towards immune checkpoint inhibitor targeted therapeutics [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 6377.

Abstract 5612: A streamlined workflow for preclinical assessment of monoclonal antibody therapies: A case study

Monoclonal antibody (mAb) therapies have become the dominant product class within the biopharmaceutical industry mainly due to their intrinsic capacity to bind endogenous immune receptors and targeted antigens. In fact, this kind of therapeutic agent accounts for one fifth of the FDA’s new drug approvals each year. In addition, their stability and specificity make them the ideal scaffold to develop more complex and efficacious drug modalities such as bispecific antibodies and antibody-drug conjugates. However, in order to advance mAb therapies to the clinic, there are a number of parameters that need to be considered during early-stage development. The purpose of this study was to showcase important preclinical characterization and efficacy experiments aimed at assessing the biological activity, binding profile, mechanism of action and in vivo potency of cetuximab, a mAb therapy. Cetuximab targets EGFR, a well characterized receptor present in the epithelial cell membrane that is overexpressed in several cancer types, such as non-small cell lung cancer, breast cancer and colorectal cancer. In normal tissues EGFR activation initiates several intracellular signaling events involved in development and homeostasis. However, when overexpressed, it stimulates the growth, metastasis and invasion of tumors. For this reason, EGFR has been considered an important target for the development of new drugs. Here we measured the binding affinity of cetuximab to two EGFR expressing cancer cell lines (A-431 and A-549) and its off-target binding to a broad range of full-length human proteins employing Retrogenix Cell Microarray Technology. Using the AlphaLISA system, we observed that cetuximab significantly inhibits EGF binding to EGFR. The consequences of cetuximab treatment on EGF binding and the initiation of the signaling cascade were investigated by looking at the phosphorylation status of EGFR via intracellular staining and flow cytometry. Moreover, we tested the ability of cetuximab to induce Antibody Dependent Cellular Cytotoxicity (ADCC) where the target cell lines were co-cultured with freshly isolated NK cells. ADCC was assessed via both flow cytometry and live cell imaging. Lastly, we studied the efficacy of cetuximab in vivo. A tumor progression mouse model generated from A-431 cells and several Patient Derived Xenografts (PDX) mouse models representing a wide variety of cancers were treated with cetuximab and a significant reduction in tumor growth was observed for most of these cancers. The in vivo efficacy correlated directly with the EGFR expression level determined by IHC. With this case study we have generated a complete and valuable preclinical data package that could be used to advance this mAb therapy into the clinic. Moreover, this study serves as the basis for a streamlined workflow for mAb lead optimization and development as well as comparability studies for biosimilars.

Citation Format: David Cobeta Lopez, Kerstin Klingner, Marie Carkill, Robert Nunan, Anya Avrutskaya, Paula Miliani de Marval, Amber Blackwell, Sarah Dawson, Donna Barnes, Jim Freeth, Deborah Bruce, Richard Bazin, René McLaughlin, Julia Schueler, Gemma Moiset, Maria L. Vlaming. A streamlined workflow for preclinical assessment of monoclonal antibody therapies: A case study [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 5612.

Abstract 2824: In vitro tumor killing assays for predicting cellular therapeutic efficacy

Cellular immunotherapy is emerging as a fifth pillar of cancer treatment. Clinical efficacy has been proven for a variety of cancers; however, its true potential has yet to be unlocked. Development of reliable and mechanistically appropriate in vitro screening assays that recapitulate in vivo immune-tumor interactions have been outpaced by in vivo living cell therapy efficacy models. Here we describe a range of in vitro primary human assays to model tumor killing by immune cells. This platform addresses multiple anti-tumor immune effector pathways and has been validated with standard of care therapeutics. Fluorescently labelled target cells (PDX-cell lines, tumor cell lines or human primary/iPSC derived cells) screened for relevant antigen expression were cultured in monolayer or spheroid forms and co-cultured with the cellular therapeutic. On target killing by effectors is driven by binding of the TCR or CAR to its cognate antigen (MHC/peptide or protein, respectively) with readouts of cell killing utilising live cell imaging (IncuCyte) and flow cytometry based approaches to measure target cell growth and apoptosis. Additional analysis of soluble mediators can determine the extent of effector cell activation. To discriminate between ‘on' and ‘off' target killing by cellular therapeutics, primary/iPSC-derived normal cell types representative of different tissue types were screened for expression of an HLA subtype capable of binding exogenously applied tumor-associated antigen (TAA) prior to co-culture. Under these conditions in the case of a TCR based cellular therapeutic, efficacy can be screened for, or in the absence of the putative TAA expression, the extent of off-target killing determined. Enhancement of tumor targeting and killing by immune cells is an attractive therapeutic modality partly due to the clinical success of checkpoint inhibitors which can enhance the activation and effector function of endogenous T/NK cells or cellular therapeutics. The presented data highlight the importance of assays which can recapitulate tumor-immune interactions and include immune effector pathways known to potentiate anti-tumor immune responses. These assays represent valuable screening tools capable of informing cellular therapeutic target selection and refinement before moving to more complex in vivo models.

Citation Format: Robert Nunan, Michelle Yap, Enrique Garcia-Alvarez, Marie Carkill, Anna Pascoe, Louise Brackenbury, Jezrom Self-Fordham, S. Rhiannon Jenkinson. In vitro tumor killing assays for predicting cellular therapeutic efficacy [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 2824.