The Development of Spec-seq and Its Application to Peripheral Blood Plasmablasts after Influenza Challenge

B cells are an integral part of the adaptive immune system and can differentiate into antibody secreting cells (ASC) in order to mediate a humoral immune response. Antibodies are soluble forms of the B cell receptor (BCR) that can bind antigen as well as elicit specific immune responses with their exchangeable constant domain. Single cell studies have extensively characterized the BCR sequence and functional capacity, but linking this to the original B cell gene expression profile has remained out of reach. To address this, we developed Spec-seq, an approach that facilitates simultaneous transcriptome and repertoire characterization at the single cell level. The unique dataset provided through this framework allowed for the development of BASIC, an algorithm to identify full-length BCR sequences from single cell RNA-sequencing data. We applied Spec-seq, and BASIC, to human peripheral blood plasmablasts seven days after influenza vaccination. We identified immunoglobulin genes as the major driver of plasmablast subpopulations, and also found differentially expressed genes between plasmablasts expressing vaccine-binding BCRs and those with vaccine-negative BCRs. The most significant of these genes have been credited in the literature with regulating antibody glycosylation, which can alter the immunogenicity of the secreted antibodies. Furthermore, we found that B cells of a single clonotype are more transcriptional similar than unrelated B cells. Overall, our findings have exposed previously unappreciated heterogeneity within plasmablast populations that are commonly utilized for the development of clinically relevant therapeutic antibodies and our Spec-seq framework will facilitate new avenues for the study of adaptive immune cells.