Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors

Patient-derived organoids (PDOs) recapitulate tumor architecture, contain cancer stem cells and have predictive value supporting personalized medicine. Here we describe a large-scale functional screen of dual-targeting bispecific antibodies (bAbs) on a heterogeneous colorectal cancer PDO biobank and paired healthy colonic mucosa samples. More than 500 therapeutic bAbs generated against Wingless-related integration site (WNT) and receptor tyrosine kinase (RTK) targets were functionally evaluated by high-content imaging to capture the complexity of PDO responses. Our drug discovery strategy resulted in the generation of MCLA-158, a bAb that specifically triggers epidermal growth factor receptor degradation in leucine-rich repeat-containing G-protein-coupled receptor 5-positive (LGR5+) cancer stem cells but shows minimal toxicity toward healthy LGR5+ colon stem cells. MCLA-158 exhibits therapeutic properties such as growth inhibition of KRAS-mutant colorectal cancers, blockade of metastasis initiation and suppression of tumor outgrowth in preclinical models for several epithelial cancer types.

Abstract 5562: A 3D image-based quantification of T cell-mediated killing of CRC organoids in the presence of immuno-modulators

BACKGROUND

Cancer immunotherapy has already yielded promising clinical results but most patients still do not respond. The mechanisms of action of these treatment modalities are also not fully understood and the progress in this direction is hampered by a lack of appropriate pre-clinical testing models. To investigate the role of novel therapeutics targeting the immune cell compartment to kill tumor cells, we developed an in vitro assay based on 3D cultures and image based analysis in a 384-wells plate format. Immune cells are added to recapitulate the tumor micro-environment and its complex interactions between different cellular players. Specifically, infiltration of immune cells into the tumoroids and their killing are visualized and measured, enabling a better understanding of the immune-modulatory profile of different treatments.

METHODS

Autologous patient derived colon organoids from normal and tumor tissue from several patients were cultured in a 3D environment. HLA-matched PBMCs with and without activation were added and immune-cell infiltration and killing of the CRC organoids was visualized in 3D using automated microscopy. Quantification of immune cell effects was achieved with morphometric analysis with OMinerTM software.

RESULTS

3D image data analysis enabled the discrimination of immune-tumor cell interactions and revealed a higher immune cell infiltration and tumoroid killing upon activation. In addition, we were able to compare both normal and tumor colon tissue from the same patient and compare between patients, demonstrating patient related differences and elucidating the effect of immune cell targeting on normal colon tissue.

CONCLUSIONS

The 3D assay presented here allows the analysis of different cell types that engage in a more realistic setting than when culturing them in traditional 2D cultures. Using image-based analysis, immune-tumor interactions can be visualized and quantified. The 3D environment, both for the cell culture and image analysis, allows for measurement of spatially resolved information, not accessible by monolayer cultures or biochemical assays. This new and innovative platform can empower immunotherapy drug developers to select the most promising candidates and better understand their mechanism of action.

Citation Format: Gera Goverse, Lidia Daszkiewicz, Kuan Yan, Mohamed Tleis, Mariusz Madej, Lucia Salinaro, Leo Price. A 3D image-based quantification of T cell-mediated killing of CRC organoids in the presence of immuno-modulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5562.

Abstract 32: Preclinical evaluation of MCLA-158: A bispecific antibody targeting LGR5 and EGFR using patient-derived colon carcinoma organoids

Background. Colorectal cancer (CRC) is the third most common cancer and remains a large unmet need. Dysregulation of Wnt and receptor tyrosine kinase (RTK) signalling pathways are important oncogenic driving events in CRC. Due to this dysregulation, Wnt target genes are expressed at higher levels in CRC particularly in tumor initiating cells. We previously performed an unbiased screen of bispecific antibodies (bAbs) targeting Wnt and RTK targets that resulted in the selection of MCLA-158.

Methods. A cohort of 32 genetically and transcriptionally annotated patient-derived colorectal cancer and normal colon organoids were used to functionally characterize responses to antibodies based on morphological changes with high content 3D imaging. Binding affinity was measured by surface plasma resonance and cell based assays. The antibody binding epitopes were mapped by shotgun mutagenesis and FACS based screening. Ligand (R-spondin or EGF) blocking activity was measured in vitro by competition for ligand binding or functional inhibition of ligand dependent growth. In vivo activity was evaluated in xenograft models generated from organoids subcutaneously implanted into immunocompromised mice. Safety was evaluated via once weekly intravenous administration of MCLA-158 to cynomolgus monkeys for 4 weeks and monitoring for pathological changes.

Results. MCLA-158, an ADCC enhanced common light chain IgG1 bispecific antibody, binds in domain III of EGFR and in the N-Cap/1st LRR of LGR5, both ligand binding regions, however, only EGF binding was blocked by MCLA-158. MCLA-158 demonstrated inhibitory activity in 74% of tumor organoids independent of KRAS mutational status but was not active on organoids of the cohort harboring both KRAS and PIK3CA mutations. MCLA-158 was significantly more active on organoids derived from tumors than from normal tissue in contrast to cetuximab, which demonstrated equivalent activity on both (range 20-100 fold, n=4). In vivo activity was evaluated against tumor organoids with different KRAS mutation status shown to be sensitive to MCLA-158 in vitro. In all cases, MCLA-158 significantly inhibited the growth of the tumor compared to both control and cetuximab treatment. Inhibitors of both the Wnt and EGFR pathways have shown significant toxicity in humans. An initial evaluation of MCLA-158 toxicity in cynomolgus monkeys did not demonstrate any pathological finding after repeated dosing at 25mg/kg.

Conclusions. MCLA-158 demonstrates superior activity compared to reference antibodies in both in vitro and in vivo tumor organoid based assays regardless of KRAS status and was well tolerated in non-human primates. These preclinical data suggest MCLA-158 could benefit patients with metastatic CRC and warrant clinical evaluation.

Citation Format: Rob Roovers, Bram Herpers, Mark James, Berina Eppink, Carme Cortina, David Maussang-Detaille, Ingrid Kolfschoten, Sylvia Boy, Marc van de Wetering, Wim De Lau, Robert Doornbos, Kuan Yan, Lucia Salinaro, Lex Bakker, john de Kruif, Hans Clevers, Robert Vries, Eduard Batlle, Leo Price, Mark Throsby. Preclinical evaluation of MCLA-158: A bispecific antibody targeting LGR5 and EGFR using patient-derived colon carcinoma organoids [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 32. doi:10.1158/1538-7445.AM2017-32

Abstract PR05: A 3D image-based phenotypic screen of bi-specific antibodies targeting stem cells in a panel of patient derived colon carcinoma organoids

Background: The high failure rate in cancer drug research has been linked to the poor predictive capacity of in vitro models using 2D cultures of cancer cell lines. Compared to 2D monolayer cultures, 3D cultured tissues show gene expression patterns, differentiation- and functional characteristics which more closely reflect the situation in vivo. Furthermore, patient-derived organoid cultures retain the gene expression profiles and histological characteristics of the original tumor tissues which are often lost during long term selection on tissue culture plastics. Organoid cultures therefore increase the scope for predicting drug responses in patients, discriminating different drug responses and flagging toxicity. We used a high content screening platform and a panel of 40 colorectal cancer organoids to characterize the responses to signaling pathway inhibitors and a panel of 545 bispecific antibodies. These antibodies comprised a HER3 or EGFR targeting arm combined with a LGR4, LGR5, ZNRF3 or RNF43 targeting arm to target stem cells. Active antibodies were rescreened and candidate leads were selected.

Results: The broad mutation spectrum of the organoids was reflected in a broad heterogeneity of organoid phenotypes. Some CRC organoids formed well-differentiated spheroids with a single lumen that resembled the phenotype of normal wild type organoids, whereas others had multiple lumens or were poorly differentiated without a luminal cavity. A rich set of morphological features was extracted from 3D image data, including organoid size and shape, planar cell polarity, lumen formation as well as cell number and nucleus shape. Some features, such as those that described lumen formation, were more sensitive in detecting drug treatment than features associated with cell proliferation, improving the sensitivity of the assay to detect active molecules. A set of 10 features was selected to create a drug response profile. We observed that the absence of activating mutations did not always correlate with sensitivity to corresponding pathway inhibitors, underscoring the need for empirical testing of drugs to predict patient sensitivity. The bispecific antibody screen was performed in two stages: a primary screen in three different tumoroid models (18,908 wells) and a validation screen in 25 different tumoroid models (23,040 wells). These screens simultaneously measured morphological alterations associated with growth, differentiation and survival (e.g. apoptosis) and identified a panel of bispecific antibodies that potently inhibited a significant majority of colorectal cancer tumoroid models tested.

Conclusions: These results demonstrate that high content screening of CRC organoids is an effective strategy to identify novel inhibitors of CRC tumor outgrowth and enable identification of bispecific antibodies that target colorectal cancer stem cells with different mutational backgrounds.

This abstract is also being presented as Poster A35.

Citation Format: Bram Herpers, Rob Roovers, Berina Eppink, Marc Van de Wetering, Kuan Yan, Lucia Salinaro, Wim De Lau, Hans Clevers, Robert Vries, Mark Throsby, Leo Price. A 3D image-based phenotypic screen of bi-specific antibodies targeting stem cells in a panel of patient derived colon carcinoma organoids. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr PR05.