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Structural dissimilarity from self drives neoepitope escape from immune tolerance

Abstract

T-cell recognition of peptides incorporating nonsynonymous mutations, or neoepitopes, is a cornerstone of tumor immunity and forms the basis of new immunotherapy approaches including personalized cancer vaccines. Yet as they are derived from self-peptides, the means through which immunogenic neoepitopes overcome immune self-tolerance are often unclear. Here we show that a point mutation in a non-major histocompatibility complex anchor position induces structural and dynamic changes in an immunologically active ovarian cancer neoepitope. The changes pre-organize the peptide into a conformation optimal for recognition by a neoepitope-specific T-cell receptor, allowing the receptor to bind the neoepitope with high affinity and deliver potent T-cell signals. Our results emphasize the importance of structural and physical changes relative to self in neoepitope immunogenicity. Considered broadly, these findings can help explain some of the difficulties in identifying immunogenic neoepitopes from sequence alone and provide guidance for developing novel, neoepitope-based personalized therapies.

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Fig. 1: The mutation in the HHATp8F neoepitope alters the surface presented to T cells without changing peptide–MHC binding.
Fig. 2: The HHATp8F neoepitope is more stimulatory with the 302TIL TCR and is recognized with higher affinity and faster association kinetics.
Fig. 3: The altered conformation in the HHATp8F neoepitope is required for TCR binding.
Fig. 4: The mutation in the HHATp8F neoepitope increases the occupancy of the Trp6 binding-competent configuration.

Data availability

Structural data, including coordinates and structure factors, are available at the Protein Data Bank (https://www.rcsb.org/) under accession codes 6UJQ, 6UJO, 6UK2 and 6UK4. Other data are available upon request.

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Acknowledgements

We thank L. Hellman for assistance with biophysical and structural work, R. Genolet for assistance with TCR sequences and C. Klebanoff for comments on the manuscript. B.M.B. acknowledges support from the NIGMS, NIH (grant no. R35GM118166). A.H. acknowledges support from the Swiss National Science Foundation (grant no. 310030–182384). D.G. acknowledges support from Swiss Cancer League (grant no. KFS-4104-02-2017). J.R.D. and G.L.J.K. acknowledge support from the Indiana CTSI, funded by the NIH (grant no. UL1TR002529). X-ray diffraction data were collected at the Advanced Photon Source, supported by DOE contract no. DE-AC02-06CH11357, and the NE-CAT and SER-CAT beamlines, supported by member institutions and NIH grants no. P30GM124165, no. S10OD021527, no. S10RR25528 and no. S10RR028976.

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Contributions

J.R.D. performed crystallography, thermal stability measurements, affinity measurements, kinetic measurements and molecular dynamics simulations. J.A.A. generated cell lines and performed measurements of T-cell function. G.L.J.K. and C.M.A. assisted with molecular dynamics simulations and their analysis. C.W.V.K. assisted with protein crystallography. D.G. and G.C. provided input on the direction of the research. A.H. and S.B. assisted with TCR construction. B.M.B. oversaw the overall project. The manuscript was written and edited by J.R.D., J.A., G.K., D.G., A.H. and B.B.

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Correspondence to Brian M. Baker.

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Extended data

Extended Data Fig. 1 Symmetry-related crystal contacts involving the neoepitope and WT peptide in their respective peptide-HLA-A*02:06 crystal structures.

The top row shows the environment of the neoepitope (left; orange) and the WT peptide (right; green), with symmetry related amino acids containing atoms within 4 Å of the peptides indicated. Atoms within 4 Å are rendered as spheres. The bottom row shows the WT peptide superimposed in the neoepitope environment (left) and the neoepitope superimposed into the WT peptide environment. In both cases, there are no steric clashes between the superimposed peptides and symmetry-related amino acids.

Extended Data Fig. 2 Isothermal calorimetric titration of HHATp8F-HLA-A*02:06 into 302TIL TCR confirms high affinity binding of the TCR to the neoantigen complex.

The fit to the data yielded a KD of 1.7 μM. Data are representative of two independent titrations with similar results (second experiment KD = 1.4 μM).

Extended Data Fig. 3 Overviews of the structures of the 302TIL TCR with the HHATp8F neoepitope and WT peptide-HLA-A*02:06 complexes.

a, Electron density (2Fo-Fc, 1σ) of the CDR loops in the neoepitope complex. b, Overview of the neoepitope ternary complex. The top shows the TCR variable domains, peptide, and the peptide-MHC binding groove (TCR constant domains, β2m, and the HLA-A*02:06 α3 domain are not shown). The bottom shows the positioning of the TCR over the peptide-MHC, with the spheres indicating the centers of mass of the Vα and Vβ domains. The TCR crossing and incident angles are indicated. c, Contact matrices for the 302TIL TCR-neoepitope-HLA-A*02:06 complex. Contacting amino acids are shown, with contacts defined as interatomic distances ≤ 4 Å. The numbers in each cell give the number of interatomic contacts for each amino acid pair; cells are colored according to the number of contacts, from white (minimum) to green (maximum). Red outlines indicate the presence of at least one hydrogen bond or salt-bridge. d–f, As in panels ac except for the complex with the WT peptide.

Extended Data Fig. 4 Comparison of the structures of the 302TIL TCR bound to the HHATp8F and WT peptide-HLA-A*02:06 complexes.

a, Superimposition of the TCR Vα/Vβ regions, peptides, and peptide binding grooves showing the overall similarities. The color scheme is given below and used for all panels. b, Cross-eyed stereo view of the TCR-peptide interface, highlighting the TCR interactions with Trp6 and Phe8/Leu8 of the peptides. c, As in panel b but rotated approximately 45° clockwise as indicated.

Extended Data Fig. 5 Binding and functional data for the HHATp8F neoepitope, WT peptide, and variants.

a, SPR binding curves for 302TIL TCR recognition of each peptide-HLA-A*02:06 complex. Each experiment consists of duplicate injections that were fit simultaneously. For each peptide, one series of duplicate injections and associated fits are shown. Experiments with peptides other than the neoepitope were fit together with a separate neoepitope titration to ensure accurate determination of weak KD values as described in ref. 29. KD values are indicated and reflect the averages and standard deviations of the number of independent experiments shown in Table 1. nbd, no binding detected; p6B, position 6 substituted with the Trp analogue Bta; RU, resonance unit. b, IL-2 production by 302TIL-transduced Jurkat 76 cells when co-cultured with HLA-A*02:06+ T2 cells pulsed with 100 μM peptide. VLF is an irrelevant negative control peptide (VLFGFTNFL). Data points are from three replicates in two independent experiments. Bars show the average of all six data points.

Extended Data Fig. 6 Comparison of tryptophan with 3-benzothienyl-l-alanine (Bta).

Chemical structures are shown on the left, with the sole difference between Trp and Bta found in the substitution of the NH in the tryptophan indole with a sulfur atom. Three dimensional structures are in the center, with an overlay on the right. The conformation of the Bta ring system is taken from ref. 43.

Extended Data Fig. 7 Conformational clustering of the Trp6 sidechain from the MD simulations of the neoepitope and WT peptide-HLA-A*02:06 complexes.

a, Conformations of the five most populated clusters in both simulations. These five accounted for >99% of the conformations sampled in both simulations. Cluster 1 (orange) matches the binding-competent conformation and cluster 4 (green) matches the WT conformation as shown in Figs. 1 and 3 and defined in Fig. 4. b, Total occupancy of the clusters in the two simulations. c, Time resolved charts of the occupancy of clusters. Each simulation enters and exits the binding competent conformation (cluster 1) multiple times, indicating that the greater occupancy of cluster 1 in the neoepitope simulation is not the result of a simulation trapped in a local minimum.

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Devlin, J.R., Alonso, J.A., Ayres, C.M. et al. Structural dissimilarity from self drives neoepitope escape from immune tolerance. Nat Chem Biol 16, 1269–1276 (2020). https://doi.org/10.1038/s41589-020-0610-1

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