Shorter TCR β-Chains Are Highly Enriched During Thymic Selection and Antigen-Driven Selection

Abstract

The adaptive immune system uses several strategies to generate a repertoire of T cell receptors (TCR) with sufficient diversity to recognize the universe of potential pathogens. However, it remains unclear how differences in the T cell receptor (TCR) contribute to heterogeneity in T cell state. In this study, we used polychromatic flow cytometry to isolate highly pure CD4 + /CD8 + naive and memory T cells, and applied deep sequencing to characterize corresponding TCR β-chain (TCRβ) complementary-determining region 3 (CDR3) repertoires. We find that shorter TCRβ CDR3s with fewer insertions were highly enriched during thymic selection. Antigen-experienced T cells (memory T cells) harbor shorter CDR3s vs. naive T cells. Moreover, the public TCRβ CDR3 clonotypes within cell subsets or interindividual tend to have shorter CDR3 length and a significantly larger size compared with “private” clonotypes. Taken together, shorter CDR3s highly enriched during thymic selection and antigen-driven selection, and further enriched in public T-cell responses. These results indicated that it may be evolutionary pressures drive short CDR3s to recognize most of antigen in nature.

Comprehensive Study of Tumor Immune Microenvironment and Relevant Genes in Hepatocellular Carcinoma Identifies Potential Prognostic Significance

“…Our research reveals that enrichment of macrophages in HCC predicts poor prognosis. T cells (CD8+ T cells and CD4+ T cells) are the key immune cells that kill tumor cells by activating the immune system (47). For this reason, novel immunotherapies, such as PD-1 and PD-L1, have been designed to modulate the activity of T cells.…”

CD4+ T cell subsets present stable relationships in their T cell receptor repertoires

“…The entire repertoire of NT was reported to be longer than the repertoire of memory 26 . However, we found that the top clones in NT were shorter than clones in other subsets in all datasets (Figure 4A; Supplemental Figure 6).…”

Preselection TCR repertoire predicts CD4+ and CD8+ T‐cell differentiation state

“…To amplify the rearranged CDR3 regions of the TCR‐β, a multiplex PCR system was designed using previously described methods. Briefly, the cDNA for each sample was amplified using a Qiagen Multiplex PCR Kit (QIAGEN) with 32 forward primers specific to the FR3 region and 13 reverse primers specific to the junction (J) region of the TCR, as published in our previous study 10,11 . The reaction conditions steps were as follows: 0·5 × Q solution, 0·2 μm Jβ R pool, 0·2 μm Vβ F pool and 1× Qiagen Multiplex PCR Master Mix.…”

“…Briefly, the cDNA for each sample was amplified using a Qiagen Multiplex PCR Kit (QIA-GEN) with 32 forward primers specific to the FR3 region and 13 reverse primers specific to the junction (J) region of the TCR, as published in our previous study. 10,11 The reaction conditions steps were as follows: 0Á5 9 Q solution, 0Á2 lm Jb R pool, 0Á2 lm Vb F pool and 19 Qiagen Multiplex PCR Master Mix. The cycling conditions were as follows: 95°for 15 min, followed by 30 cycles of 94°for 30 s, 60°for 90 s, 72°for 30 s, plus a final extension of 5 min at 72°.…”

“…Furthermore, much of the TCR-b CDR3 diversity was created by a template-independent insertion of nucleotides at the Vb-Db and Db-Jb junctions by terminal deoxynucleotidyl transferase (Tdt). 10 The frequency at which Tdt inserts each of the four nucleotides (G, C, A and T) was estimated, and the insertion frequencies of the four nucleotides exhibited a significantly positive relationship between the pre-and post-selection TCR-b repertoires, regardless of the Vb-Db ( Fig. S11a-d) or Db-Jb junctions (Fig.…”