Development of DNA-Labeled Antibody Mimetics as Low-Cost, High-Performance Reagents for Single Cell Analysis of Membrane Proteins

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Averaging signals over a population of cells often misses biologically relevant variation among single cells. New approaches are emerging with the power to identify differences between individual cells that are not detectable in studies of entire populations. One approach, called single‐cell RNA‐seq, has rapidly been adopted in the scientific community. Single‐cell RNA‐seq is now increasingly performed simultaneously with the measurement of protein levels. Recent technologies use DNA‐labeled antibodies to measure levels of 10‐100 proteins in the context of a genome‐wide analysis. However, these technologies have not yet been widely adopted because of the cost and effort required and the relatively small number of proteins that can be measured. Significant cost and effort are required to prepare DNA‐labeled antibodies which have limited commercial availability. Furthermore, results with antibodies are sometimes imprecise because antibodies have multiple binding sites for their targets and multiple conjugation sites for their DNA‐label. We propose to develop a technology platform optimized for DNA‐based detection of proteins in single‐cell experiments. The core of our platform is a potent and selective single domain antibody mimetic called a nanoCLAMP that can be customized for specific applications and produced inexpensively. For single‐cell applications, nanoCLAMPs have the potential for higher performance and lower cost than traditional antibodies. Unlike traditional antibodies, binding events are straightforward to interpret because nanoCLAMPs are monomers with a single target binding site and a single site for DNA‐labeling. nanoCLAMPs are also economical to develop and use because they can be isolated without the need to immunize animals and can be produced in bacteria at high levels. This work proposes 3 specific aims: 1. Generate a test set of 5‐10 nanoCLAMPs against cell surface proteins. 2. Optimize DNA labeling and cell‐binding conditions. 3. Compare the performance of nanoCLAMPs to traditional antibodies in single‐cell experiments and assess the feasibility of scale‐up. Successful completion of these aims will establish the feasibility of a technology platform with the potential to accelerate the adoption of simultaneous single‐cell RNA and protein analyses.