Class II Major Histocompatibility Complex Mutant Mice to Study The
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Class II major histocompatibility complex mutant mice PNAS PLUS to study the germ-line bias of T-cell antigen receptors Daniel Silbermana,b, Sai Harsha Krovib, Kathryn D. Tuttleb, James Crooksc, Richard Reisdorphd, Janice Whitea, James Grossa, Jennifer L. Matsudaa, Laurent Gapinb, Philippa Marracka,b,e,1, and John W. Kapplera,b,e,1 aDepartment of Biomedical Research, National Jewish Health, Denver, CO 80206; bDepartment of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045; cDivision of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO 80206; dPharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045; and eHoward Hughes Medical Institute, National Jewish Health, Denver, CO 80206 Contributed by Philippa Marrack, July 6, 2016 (sent for review March 2, 2016; reviewed by Erin J. Adams and Martin Flajnik) The interaction of αβ T-cell antigen receptors (TCRs) with peptides anism termed “negative selection” (13, 14). The remaining T bound to MHC molecules lies at the center of adaptive immunity. cells go on to mature and form the peripheral T-cell repertoire. Whether TCRs have evolved to react with MHC or, instead, pro- The effect of positive and negative thymic selection on limiting cesses in the thymus involving coreceptors and other molecules the T-cell repertoire has made it difficult to test directly whether select MHC-specific TCRs de novo from a random repertoire is a germ-line features of TCRs and MHC molecules have been con- longstanding immunological question. Here, using nuclease-tar- served to promote their interaction. However, some data consistent geted mutagenesis, we address this question in vivo by generating with this notion have accumulated over the past several decades three independent lines of knockin mice with single-amino acid through sequencing, X-ray crystallographic, mutational, and de- mutations of conserved class II MHC amino acids that often are velopmental studies. For example, random examination of mouse – T cells before positive selection showed a high frequency of MHC- involved in interactions with the germ-line encoded portions of – TCRs. Although the TCR repertoire generated in these mutants is reactive cells (15 17). In mice constructed to allow positive selec- similar in size and diversity to that in WT mice, the evolutionary tion but incomplete negative selection, an even higher frequency of bias of TCRs for MHC is suggested by a shift and preferential use of generically MHC-reactive T cells was observed (18). Structural and some TCR subfamilies over others in mice expressing the mutant sequencing studies of MHC molecules have shown that the great majority of their polymorphisms are within the peptide-binding class II MHCs. Furthermore, T cells educated on these mutant MHC INFLAMMATION groove, not on the tops of the MHC α-andβ-chain helices that IMMUNOLOGY AND molecules are alloreactive to each other and to WT cells, and vice interact with TCRs (Table 1). The CDR1 and CDR2 loops of versa, suggesting strong functional differences among these rep- TCRsaremuchlessvariableinlengththanthoseofIgs(19).Inthe ertoires. Taken together, these results highlight both the flexibility dozens of structures of peptide–MHC/TCR complexes that have of thymic selection and the evolutionary bias of TCRs for MHC. been solved, a diagonal orientation of the TCR is nearly always seen. This orientation usually causes the somatically generated T-cell receptor | MHC | evolution | mutation | variable region CDR3s to be focused on the peptide and the germ-line–encoded CDR1 or CDR2 amino acids, especially those of CDR2, to be he genes for immunoglobulins (Igs), αβ T-cell receptors docked on the conserved portions of the MHC helices (9). T(TCRs), and antigen-presenting MHC proteins appeared at Mutation of these TCR amino acids impairs T-cell recognition least 450 million years ago in the cartilaginous fish and are present of the ligand and affects thymic development of the T cells in in all modern vertebrates (1–3). The more primitive hagfish and vivo (8, 20–22). Some of these germ-line TCR amino acids can lampreys lack these genes and have an adaptive immune system be traced back to the TCRs of fish, and, despite their overall comprised of unrelated proteins (4). The main ligands for αβ TCRs are short peptides derived from self and foreign proteins, Significance captured in a specialized groove of MHC class I (MHCI) and class II (MHCII) molecules and presented to T cells (5, 6). Functional The evolutionary hypothesis for T-cell antigen receptor–pep- Igs and TCRs are created by very similar recombination mecha- tide major histocompatibility complex (TCR–pMHC) interaction nisms involving fusion of V, J, and sometimes D gene segments posits the existence of germ-line–encoded rules by which the with additional variations at the junctions to create an enormous TCR is biased toward recognition of the MHC. Understanding potential repertoire of Igs and TCRs, suggesting a common, un- these rules is important for our knowledge of how to manip- known evolutionary origin for these loci. ulate this important interaction at the center of adaptive im- These observations have raised several unanswered questions. munity. In this study, we highlight the flexibility of thymic For example,why did a separate TCR-rearranging gene system – selection as well as the existence of these rules by generating develop for lymphocytes recognizing peptide MHC ligands? How knockin mutant MHC mice and extensively studying the TCR did the extraordinarily polymorphic MHC genes stay functionally repertoires of T cells selected on the mutant MHC molecules. connected to TCR genes throughout 450 million years of evolu- Identifying novel TCR subfamilies that are most evolutionarily tion? One long-standing hypothesis has been that certain features conserved to recognize specific areas of the MHC is the first of TCRs and MHC molecules are evolutionarily conserved to step in advancing our knowledge of this central interaction. promote their interaction (7–10). Like Igs, the antigen-recogni- tion portions of TCRs are partially encoded in the comple- Author contributions: D.S., S.H.K., L.G., P.M., and J.W.K. designed research; D.S., S.H.K., mentary determining region (CDR) CDR1 and CDR2 loops of K.D.T., R.R., and J.W. performed research; D.S., S.H.K., J.G., J.L.M., and J.W.K. contributed germ-line TCR Vα (TRAV) and Vβ (TRBV) genes and are new reagents/analytic tools; D.S., J.C., and L.G. analyzed data; and D.S., S.H.K., L.G., P.M., partially generated by somatic recombination processes that and J.W.K. wrote the paper. form the CDR3 loops. This initial repertoire is culled dramati- Reviewers: E.J.A., University of Chicago; and M.F., University of Maryland. cally during T-cell development in the thymus. First, only those T The authors declare no conflict of interest. cells whose TCRs have at least some minimal affinity for the self- Freely available online through the PNAS open access option. – peptide MHC molecules expressed in the thymus are positively 1To whom correspondence may be addressed. Email: [email protected] or kapplerj@ selected for further development (11, 12). The T cells in this njhealth.org. population whose TCRs have too high an affinity for these self- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. peptide–MHC molecules are eliminated by an apoptotic mech- 1073/pnas.1609717113/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1609717113 PNAS Early Edition | 1of10 Downloaded by guest on September 29, 2021 Table 1. Alignment of I-A haplotype helix residues with alanine (A), and alanines were replaced with glutamine (Q). Alanine was chosen as a neutral, frequently used mutational re- placement, and glutamine was chosen because it is already present at the other positions on the helix and thus would not greatly alter the chemistry at the surface of the protein. Genes encoding either the mutant I-Ab α-orβ-chain, paired with the corresponding WT I-Ab α or β gene, were transduced into an MHCII-deficient B-cell lymphoma, M12.C3 (27, 28), to create APCs expressing the mu- tant I-Ab molecules. M12.C3 cells, derived from an H-2d mouse, lack an I-Ad β-chain but express a functional I-Ad α-chain from the original M12 BALB/c lymphoma. This I-Ad α-chain can some- times pair with some other introduced I-A β-chains, including that of I-Ab. For this reason we prepared M12.C3 cells transduced with only the WT I-Ab β-chain to control for the possible activity of the I-Ad/b mixed molecule. M12.C3 cells transduced with both of the WT I-Ab genes served as a positive control, and M12.C3 cells with b α *The solvent-exposed residues of I-Aα or I-Aβ mutated in this study are only the WT I-A -gene were also used as a negative control. numbered. All the M12.C3 transductants were cloned at limiting dilution, † b Consensus sequence. and surface expression of I-A was confirmed by flow cytometry. ‡Differences from consensus sequence. Because each mutation might have affected the epitopes recog- nized by individual mAb differently, we stained the cells using a variety of anti–I-Ab–specific mAbs. Fig. 1B shows data for the weak sequence homology, substitution of fish V segments for the 227 mAb, the antibody least affected by the mutations. With this mouse V segments preserves antigen recognition of the mouse peptide–MHC complex (23). Finally, although RAG-mediated rearrangement makes the CDR3 more diverse, the CDR1 and CDR2 loops in TCRs, unlike those in Igs, do not undergo an- tigen-selected somatic mutation; thus they keep their germ-line sequence and antigen-driven responses throughout develop- ment, suggesting a conserved function (24, 25).