Abstract
The diversity of the T cell receptor (TCR) complementarity determining region 3 (CDR3) repertoire is the result of random combinations, insertions and deletions during recombination of the germline V, D and J gene fragments. During evolution, some human TCR beta chain variable (TRBV) pseudogenes have been retained. Many previous studies have focused on functional TRBV genes, while little attention has been given to TRBV pseudogenes. To describe the compositional characteristics of TRBV pseudogene rearrangements, we compared and analysed TRBV pseudogenes, TRBV open reading frames (ORFs) and functional TRBV genes via high-throughput sequencing of DNA obtained from the peripheral blood of 4 healthy volunteers and 4 patients. Our results revealed several differences in J and D gene usage. The V deletion distribution profile of the pseudogenes was significantly different from that of the ORFs and functional genes. In addition, arginine, lysine and cysteine were more frequently used in putative CDR3 pseudogene rearrangements, while functional rearrangements used more leucine. This study presents a comprehensive description of the compositional characteristics of peripheral TRBV pseudogene rearrangements, which will provide a reference for further research on TRBV pseudogenes.
Highlights
T cell receptor (TCR), which is located in the T lymphocyte membrane, is an important functional receptor that participates in the cellular immunological response
This disparity was enlarged in the disease group due to the expansion of TRBV21-1 (1.9% VS 0.4%), which may be related to the disease condition
These results suggested that the TCR beta chain variable (TRBV) pseudogene rearrangements and functional gene rearrangements may have significant differences in composition and prompted us to compare their compositional characteristics
Summary
T cell receptor (TCR), which is located in the T lymphocyte membrane, is an important functional receptor that participates in the cellular immunological response. The “functional gene” identifies the molecule type or the gene functionality in the undefined or germline configuration, which has an ORF without a stop codon in its coding region and for which there is no described defect in the splicing sites, recombination signals, and/or regulatory elements. Rezvany MR et al found that the TRBV21-1 pseudogene stimulated by leukaemic B cells in CD4+ and CD8+ T cells showed oligoclonal expansion[8] These early studies were based on analysis of the intrinsic defects in the TRBV pseudogene sequences or indirectly demonstrated the in-frame and out-of-frame rearrangements of the TRBV pseudogenes and examined whether the TRBV pseudogenes show clonal or oligoclonal mRNA expression under various pathological conditions. There has been no systematic analysis of the characteristics of TRBV pseudogenes
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