Deep-mining the antibody repertoires of transgenic mouse models with high-throughput single cell BCR and whole transcriptome sequencing 3955

Description Transgenic mouse models are excellent tools to model human antibody response against antigens of choice, given their ability to undergo diversification, in vivo affinity maturation, clonal selection and clonal expansion in their natural immune environment. Current antibody discovery methods lack the scale required to fully screen the antibody repertoire of transgenic mouse models to uncover the maximum number of desirable antibody hits per discovery campaign. Here, we demonstrate our novel combinatorial barcoding approach to enable high-throughput single cell BCR and whole transcriptome profiling of transgenic mouse samples with unprecedented sensitivity, scalability, and flexibility. As a proof of concept, we profiled over 1 million cells from multiple transgenic mice that were either naive or immunized with antigens of interest to obtain hundreds of thousands of paired BCR clonotypes. Using the whole transcriptome data we detected all B cell subpopulations including plasma cells at single cell resolution. We then used the paired heavy and light chain BCR data to detect productive chains in the majority of B cells revealing both unique and expanded clonotypes. In the expanded clonotype pool we found specific patterns of VDJ utilization and amino acid motifs compared to the naive pool. This method paves the way for high throughput screening of antibody repertoires from transgenic mice to allow for deep mining of antibodies.