scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains in human and mice

Abstract The binding of T cell receptor (TCR)/B cell receptor (BCR) CDR3 with linear or conformational epitopes is a prerequisite for the adaptive immune response. The rules for CDR3 length pairing and the amino acid (AA) distributions in the prioritized rearrangement of the β chain (or heavy chain) and subsequent rearrangement of the α chain (or light chain) during the process of germline V(D)J gene rearrangement and self-tolerance selection to form the T- or B-cell CDR3 repertoire are currently unknown. Single-cell VDJ sequencing can provide abundant information on CDR3 sequences in paired chains. In this study, the paired-chain CDR3 sequences of central and peripheral T and B cells in humans and mice were analyzed according to single-cell VDJ sequencing data. This is the first study to find that T cells with β chains longer than paired α chains and B cells with heavy chains longer than paired light chains have absolute advantages. The proportion of T cells with length differences of three or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice, and the proportion of B cells with length differences of six or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice. The CDR3 length range of the β chain was narrower than that of the α chain, while the heavy chain had a much wider range than the light chain. The CDR3 length in human TCRs and BCRs was greater than that in mice. Extreme length differences were found between paired chains in both human and mouse T and B cells. There were significant differences in the range of pairing length, AA distribution, hydrophobicity, and polarity of the paired-chain CDR3 region in 5 chains (β, α, H, κ, and λ). Human TCR and BCR paired CDR3 sequences exhibited greater plasticity than those of mice. This study reveals new ideas about the molecular mechanisms of TCR and BCR responses to different antigenic epitopes. Our innovative findings offer novel perspectives and techniques for examining V(D)J rearrangement and selection mechanisms in T and B cells. These advancements enable us to analyze antigenic epitopes targeted by TCRs and BCRs, and further, to explore the genetic evolution of T and B cell responses across diverse animal species. Graphical Abstract scRNA-seq the TCR and BCR CDR3 repertoires of 35 samples from the central and peripheral tissues of humans and mice. It provides an opportunity to reveal the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains.