Comprehensive analysis of αβT-cell receptor repertoires reveals signatures of thymic selection

Daniil V. Luppov^1,2,3Elizaveta K. Vlasova^1,4Dmitriy M Chudakov^1,5,6,7,8Mikhail Shugay^1,6*

• ¹Research Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Moscow Oblast, Russia
• ²Department of Biological and Medical Physics, School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Oblast, Russia
• ³Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, I.M. Sechenov First Moscow State Medical University, Moscow, Moscow Oblast, Russia
• ⁴ITMO University, Saint Petersburg, Saint Petersburg, Russia
• ⁵Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Olomouc, Czechia
• ⁶Department of Genomics of Adaptive Immunity, Institute of Bioorganic Chemistry (RAS), Moscow, Moscow Oblast, Russia
• ⁷Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
• ⁸Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates

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 serve as a backbone of adaptive immunity. In 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 gene 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 together 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 TCR, the "holes" in TCR repertoire induced by negative selection can be related to Arginines in the 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.