Microenvironment on Demand (MOD): A platform for single-cell cytotoxicity assays

ABSTRACT Scribe Biosciences are leading experts in the field of droplet microfluidics and have developed a best-in-class droplet manipulation platform, Microenvironment on Demand (MOD), that can currently assemble more than 100k paired-cell assays in under 3 hours, with proven proof of concept. Using this innovative technology, this SBIR Phase 1 project proposes the development of a new functional screening platform that builds single-cell combinatorial assays to be used for workflows for cell therapy candidates, to be tested here with CAR T cells. The development of such a platform to reliably, consistently, and repeatably interrogate the activity of single CAR T cells would answer a significant research need: Currently, even though CAR T cell-based therapeutics is the largest category of immune-oncology agents under clinical development, there are considerable knowledge gaps regarding many key mechanisms governing their activity, compounded by limited industry-standard candidate discovery methods (bulk averages across an assay) which do not provide adequate information on important factors. MOD represents an evolutionary advancement in the capability to build droplet-based cell assays with precision and scale, effectively integrating assay construction, readouts, hit selection, and sample prep into a single workflow and instrument. MOD co-encapsulates effector and target cells in the same microfluidic droplet, easing identification of cytotoxic effector cells, and utilizes flow cytometry-style detection and sorting, so it is readily scalable for high throughput. The approach for this project has been informed by previous work developing assays on the MOD platform. Bulk interaction studies will be used to study cell killing kinetics and different assay reagents; results will be used to build robust cytotoxicity droplet-based screening assays for several model systems and quantify their performance. Natural killer (NK) cells and cytotoxic T-cells will be used, specifically NK92MI (IL-2 independent NK cell line) with K562 targets and anti-CD19 CAR-Ts with (CD19+) Nalm 6 targets. The second aim will seek to understand the sensitivity of the MOD assay workflow by benchmarking the droplet assay systems using spike-in experiments, using a cell system and assay reagent suitable for fast cell killing and slow killing assays (tested separately). The limits of the technology will be characterized as the relative amount of effector-cell containing droplets is incrementally reduced from 25% to1%. By building out assays for both fast and slow cell killing, the technology will be ready to be applied to many different interacting cell systems. Success of this functional screen assay will be determined by detection and sorting 10 hits of target cell killing by a 1% effector cell spike-in in both models, and will enable advancement to a Phase 2 study with diverse libraries and genomic integration. Successful MOD-enabled cytotoxicity assays could create a new paradigm in the type of specific data that can be extracted from interaction assays, and would significantly ease the identification of superior CAR T cell products with enhanced potency and persistence to improve efficacy and durability, and increase the breadth of treatable malignancies.