Comparison of T-cell receptor β chain variable region 23-1 open reading frame and 3-1 F CDR3 repertoire in cDNA and gDNA from peripheral blood mononuclear cells of healthy volunteers by high-throughput sequencing

The TRBV germline gene can be classified into three types: open reading frame (ORF), functional gene (F), and pseudogene (P); however, the differences and connections among ORF, functional gene, and pseudogene rearrangements and expression characteristics remain unclear. Here, we compared the characteristics of the CDR3 repertoire that was rearranged by TRBV23-1(ORF) and TRBV3-1(F) in four cDNA samples and six gDNA samples from healthy volunteers. In this study, we show that the frequencies of in-frame sequences in the TRBV23-1 complementarity determining region 3 (CDR3) repertoire were significantly lower than those in the TRBV3-1 CDR3 repertoire. The TRBV23-1 CDR3 repertoire, which differed from the TRBV3-1 in-frame and out-of-frame CDR3 repertoire, consisted of 1/3 in-frame sequences and 2/3 out-of-frame sequences. The usage of TRBD1 was higher than that of TRBD2 in the TRBV23-1 in-frame and out-of-frame CDR3 repertoire. In four cDNA samples from PBMCs, the TRBV23-1 in-frame and out-of-frame CDR3 repertoire showed a longer N2 relative to that of N1. Therefore, our results demonstrate that the mechanisms of rearrangement in the TRBV23-1 and TRBV3-1 CDR3 repertoire were different, and thus offered new ideas and methods to resolve the discrepancies in reports on the functionality of TRBV23-1 and to better understand the mechanisms underlying VDJ recombination.