Analysis of the Repertoire Features of TCR Beta Chain CDR3 in Human by High-Throughput Sequencing

Abstract

Background/aims: To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of T-cell receptors, collectively referred to as the TCR repertoire. Assessment of the repertoire features of TCR is vital for us to deeper understand of immune behaviour and immune response.

Methods: In this study, we used a combination of multiplex-PCR, Illumina sequencing and IMGT (ImMunoGeneTics)/HighV-QUEST for a standardized analysis of the repertoire features of TCR beta chain in the blood of healthy individuals, including the repertoire features of public TCR complementarity-determining regions (CDR3) sequences, highly expanded clones, long TCR CDR3 sequences.

Results: We found that public CDR3 sequences and high-frequency sequences had the same characteristics, both of them had fewer nucleotide additions and shorter CDR3 length, which were closer to the germline sequence. Moreover, our studies provided evidence that public amino acid sequences are produced by multiple nucleotide sequences. Notably, there was skewed VDJ segment usage in long CDR3 sequences, the expression levels of 10 TRβV segments, 7 TRβJ segments and 2 TRβD segments were significantly different in the long CDR3 sequences compared to the short CDR3 sequences. Moreover, we identified that extensive N additions and increase of D gene usage contributing to TCR CDR3 length, and observed there was distinct usage frequency of amino acids in long CDR3 sequences compared to the short CDR3 sequences.

Conclusions: Some repertoire features could be observed in the public sequences, highly abundance clones, and long TCR CDR3 sequences, which might be helpful for further study of immune behavior and immune response.