Cross-reactive public TCR sequences undergo positive selection in the human thymic repertoire
Mohsen Khosravi-Maharlooei, … , Todd M. Brusko, Megan Sykes
Mohsen Khosravi-Maharlooei, … , Todd M. Brusko, Megan Sykes
Published March 28, 2019
Citation Information: J Clin Invest. 2019;129(6):2446-2462. https://doi.org/10.1172/JCI124358.
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Research Article Autoimmunity Immunology

Cross-reactive public TCR sequences undergo positive selection in the human thymic repertoire

Abstract

We studied human T cell repertoire formation using high-throughput T cell receptor β (TCRβ) complementarity-determining region 3 (CDR3) sequencing in immunodeficient mice receiving human hematopoietic stem cells (HSCs) and human thymus grafts. Replicate humanized mice generated diverse and highly divergent repertoires. We observed repertoire narrowing and increased CDR3β sharing during thymocyte selection. Whereas hydrophobicity analysis implicated self-peptides in positive selection of the overall repertoire, positive selection favored shorter shared sequences that had reduced hydrophobicity at positions 6 and 7 of CDR3βs, suggesting weaker interactions with self-peptides than were observed with unshared sequences, possibly allowing escape from negative selection. Sharing was similar between autologous and allogeneic thymi and occurred between different cell subsets. Shared sequences were enriched for allo–cross-reactive CDR3βs and for type 1 diabetes–associated autoreactive CDR3βs. Single-cell TCR sequencing showed increased sharing of CDR3αs compared with CDR3βs between mice. Our data collectively implicate preferential positive selection for shared human CDR3βs that are highly cross-reactive. Although previous studies suggested a role for recombination bias in producing “public” sequences in mice, our study is the first to our knowledge to demonstrate a role for thymic selection. Our results implicate positive selection for promiscuous TCRβ sequences that probably evade negative selection, given their low affinity for self-ligands, in the abundance of “public” human TCRβ sequences.

Authors

Mohsen Khosravi-Maharlooei, Aleksandar Obradovic, Aditya Misra, Keshav Motwani, Markus Holzl, Howard R. Seay, Susan DeWolf, Grace Nauman, Nichole Danzl, Haowei Li, Siu-hong Ho, Robert Winchester, Yufeng Shen, Todd M. Brusko, Megan Sykes

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Figure 1

Experimental design and clonality scores.

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Experimental design and clonality scores. (A–C) Generation of humanized ...
(A–C) Generation of humanized mice for experiments 1, 2, and 3. Cell populations were sorted for sequencing at 14, 20, and 22 weeks after transplantation, respectively. (D–F) Clonality scores for cell populations in experiments 1, 2, and 3 at the nucleotide nonproductive (Nt nonproductive), Nt productive (Nt productive), and aa levels (mean ± SEM, except for experiment 3, which shows individual animals). Paired t tests were performed to compare the clonality of each sequence set within each cell population. Paired t tests with Bonferroni’s multiple testing correction were performed to compare different cell populations in experiment 2. *P < 0.05 and **P < 0.01, by paired t test (paired by mouse, with Bonferroni’s multiple-testing correction). P. CD8, peripheral CD8+; P. CD4, peripheral CD4+. (G) Scores for aa clonality of grafted thymi and the original autologous thymus in experiment 2. (H) Expression of TdT in DP thymocytes of fetal (n = 3, gestational ages of 17, 20, and 21 weeks), postnatal (n = 4, age 4 months, 6 months, 13 years, and 17 years), and grafted human thymi in humanized mice (n = 3, at 18, 26, and 33 weeks after transplantation). *P < 0.05, by unpaired t test.