Thymic selection is crucial for forming a pool of T-cells that can efficiently discriminate self from non-self using their T-cell receptors (TCRs) to develop adaptive immunity. In the present study we analyzed how a diverse set of physicochemical and sequence features of a TCR can affect the chances of successfully passing the selection. On a global scale we identified differences in selection probabilities based on CDR3 loop length, hydrophobicity, and residue sizes depending on variable genes and TCR chain context. We also observed a substantial decrease in N-glycosylation sites and other short sequence motifs for both alpha and beta chains. At the local scale we used dedicated statistical and machine learning methods coupled with a probabilistic model of the V(D)J rearrangement process to infer patterns in the CDR3 region that are either enriched or depleted during the course of selection. While the abundance of patterns containing poly-Glycines can improve CDR3 flexibility in selected TCRs, the "holes" in the TCR repertoire induced by negative selection can be related to Arginines in the (N)-Diversity (D)-N-region (NDN) region. Corresponding patterns were stored by us in a database available online. We demonstrated how TCR sequence composition affects lineage commitment during thymic selection. Structural modeling reveals that TCRs with "flat" and "bulged" CDR3 loops are more likely to commit T-cells to the CD4+ and CD8+ lineage respectively. Finally, we highlighted the effect of an individual MHC haplotype on the selection process, suggesting that those "holes" can be donor-specific. Our results can be further applied to identify potentially self-reactive TCRs in donor repertoires and aid in TCR selection for immunotherapies.

• Keywords
• HLA alleles, T-cell immunity, T-cell receptor repertoire, immune repertoire analysis, immune repertoire sequencing, thymic selection,
• MeSH
• Complementarity Determining Regions genetics   immunology   chemistry   MeSH
• Humans MeSH
• Receptors, Antigen, T-Cell, alpha-beta * genetics   immunology   chemistry   MeSH
• Thymus Gland * immunology   cytology   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Complementarity Determining Regions MeSH
• Receptors, Antigen, T-Cell, alpha-beta * MeSH

The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.

• Keywords
• CDR3 properties, TCR repertoire, helper CD4+ subsets, human, immunology, inflammation, plasticity of CD4+ subsets,
• MeSH
• Cell Lineage immunology   MeSH
• CD4-Positive T-Lymphocytes immunology   MeSH
• Humans MeSH
• Receptors, Antigen, T-Cell, alpha-beta immunology   MeSH
• T-Lymphocyte Subsets immunology   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Receptors, Antigen, T-Cell, alpha-beta MeSH