Micro-capsule technology for high-throughput analyses of cell-cell interactions

Project Summary This proposal develops a novel technology to enable analysis of millions and eventually hundreds of millions of live cell-cell interactions in parallel. These tools will address a major unmet need, with future potential applications including but not limited to screening functional antibodies and peptides, evaluating ligand-

receptor specificity, and determining affinities in cell adhesion. The technology is embodied by micro-capsules: semi-permeable compartments composed of a thin shell and a hollow core, which can be generated extremely rapidly around cells. Micro-capsules are resilient and exchange small molecules with surrounding media. They allow long-term cell growth, as well as multiple sequential steps

of imaging, treatment, cell fixation, staining, and sorting, including steps that are difficult or impossible to carry out today on defined cell mixtures at high-throughput. In this proposal, we build on proof-of-concept data to now establish and benchmark two prototype methods that will enable screening and mapping cell interactions at a scale that is 100-10,000-fold greater than is

possible with existing plate-based or microfluidic methods, at lower cost and in less time. We use receptor agonist/antagonist screening and mapping as test cases that allow defining clear performance indicators, including false-positive and false-negative rates of the method. The two methods entail (1) high-throughput

screening of cell-cell interactions, and (2) high-throughput mapping of cell-cell interactions. “Screening” focuses on selecting particular desirable interactions from a large pool, while “Mapping” refers to the task of systematically associating variation in an input variable (e.g. DNA sequence or signaling environment) with an

output (e.g. cell activity). Currently, the only methods for systematically mapping cell-cell interactions require using micro-well plates at low throughput. In addition, in parallel to developing the prototype platforms, we will continue to develop capsule chemistries and microfluidic capabilities that will enable faster screening, different capsule sizes suitable for working with

bacteria (small) to organoids (large) and multiple cell types, and to enable different screening outputs. These capabilities are not needed for the prototypes but will generalize them. If successful, we will have developed, optimized and benchmarked the prototype systems to the point where they are ready for earnest application to problems in high-throughput screening and systematic mapping of

cell-cell interactions. To do so, we focus on systematically problem-solving assay design, and we incorporate benchmarks throughout. The proposed research will significantly accelerate our ability to both gain basic quantitative insights into cell-cell interactions in health and disease, and to enable new platforms for

therapeutic discovery.