Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3′-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3′-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination. ### Competing Interest Statement JCL has interests in Sunflower Therapeutics PBC, Honeycomb Biotechnologies, OneCyte Biotechnologies, SQZ Biotech, Alloy Therapeutics, QuantumCyte, Amgen, and Repligen (these interests are reviewed and managed under Massachusetts Institute of Technology policies for potential conflicts of interest); in addition, he receives sponsored research support at Massachusetts Institute of Technology from Amgen, the Bill and Melinda Gates Foundation, Biogen, Pfizer, Sartorius, Mott Corp, TurtleTree, Takeda, and Sanofi, and his spouse is an employee of Sunflower Therapeutics PBC. JK, MM, SS, LJ, NS, IK, and LC are employees of Pfizer and may, as a consequence, be shareholders. Pfizer was involved in the design, analysis, and interpretation of the data in this research study, the writing of this report, and the decision to publish. The other authors declare no conflicts of interest.