Neoantigen quality predicts immunoediting in survivors of pancreatic cancer

To identify the edited neoantigens, we extended our previous neoantigen quality model4,5 that quantifies the immunogenic features of a neoantigen to propose that two competing outcomes determine whether a neoantigen is high-quality—whether the immune system recognizes or tolerates a neoantigenic mutation (Fig. 3a). To estimate the likelihood the immune system recognizes a neoantigen, we measure the sequence similarity of the mutant neopeptide (pMT) to known immunogenic antigens. This infers the ‘non-self’ recognition potential R of pMT, a proxy for peptides within the recognition space of the T cell receptor (TCR) repertoire.

By contrast, we posit that the immune system can also fail to discriminate pMT from its wild-type (WT) peptide (pWT), and therefore tolerate it as ‘self’. The immune system must therefore exert greater self discrimination D (Fig. 3a) in tumours to overcome the principles of negative T cell selection, the adaptation that limits autoreactivity to host tissues. We approximate the D between pWT and pMT by two features—differential MHC presentation and differential T cell reactivity. Differential MHC presentation of pWT and pMT (({K}_{{rm{d}}}^{text{WT}}/{K}_{{rm{d}}}^{text{MT}})), previously introduced as the MHC amplitude A (refs. 4,5), estimates the availability of T cells to recognize pMT. If pWT is not presented to T cells in the thymus or the periphery (as with a high ({K}_{{rm{d}}}^{text{WT}}), which implies poor pWT–MHC binding), pWT-specific T cells escape negative selection to expand the peripheral T cell precursor pool available to recognize a pMT presented on MHC (low ({K}_{{rm{d}}}^{text{MT}}))20. Here we extend this concept and introduce cross-reactivity distance C, a new model term that estimates the antigenic distance required for T cells to discriminate between pMT and pWT. Thus, self discrimination D = log(A) + log(C) is a proxy for peptides outside the toleration space of the TCR repertoire. In summary, we define neoantigen quality as Q = R × D (Fig. 3a), now with components that estimate whether a neoantigen can be recognized as non-self and discriminated from self.

To model C, we leveraged recent findings that conserved structural features underlie TCR–peptide recognition. Specifically, the binding domains of peptide-degenerate TCRs21,22 and TCR-degenerate peptides23 share common amino acid motifs, suggesting that T cell cross-reactivity between pMT and pWT could estimate the relative C of different neoantigenic substitutions (Fig. 3b). We selected an HLA-A*02:01-restricted strong epitope (NLVPMVATV (NLV)) from human cytomegalovirus24 that was previously used to model TCR–peptide degeneracy21,22 as a model pWT, and three NLV-specific TCRs (Extended Data Fig. 4a–c). We then varied the NLV peptide by every amino acid at each position to model pMT substitutions, and compared how TCRs cross-react between each pMT and its pWT across a 10,000-fold concentration range where pWT changes maximally altered T cell activation (Fig. 3b). We observed that substitutions were either highly, moderately or poorly cross-reactive (Fig. 3c, d), and the cross-reactivity pattern depended on the substituted position and residue (Extended Data Fig. 5a). Interestingly, we found similar patterns of cross-reactivity between a model HLA-A*02:01-restricted weaker pWT epitope in the melanoma self-antigen gp10025,26 (Extended Data Figs. 4d and 5b), three pWT-specific TCRs and single-amino-acid-substituted pMTs, suggesting that conserved substitution patterns define C (Fig. 3e and Extended Data Fig. 5b). Thus, we quantified the cross-reactivity distance C between a pWT and its corresponding pMT as (,Cleft({{bf{p}}}^{{rm{WT}}},{{bf{p}}}^{{rm{MT}}}right)={{rm{EC}}}_{50}^{{rm{MT}}}/{{rm{EC}}}_{50}^{{rm{WT}}}). We chose the half maximal effective concentration (EC50) to model C, as T cell activation to pWT was consistently a sigmoidal function (Extended Data Figs. 4c, d and 6a, b) described by a Hill equation, where EC50 determines how a ligand activates a receptor. We next estimated the EC50 of all 1,026 TCR–pMT pairs to infer a model for C that estimates whether a neoantigenic substitution is cross-reactive (and therefore tolerated) based on the substituted amino acid position and residue (Extended Data Figs. 6a, b and 7a, b). We then tested whether C predicted cross-reactive substitutions in an HLA-B*27:05-restricted neopeptide–TCR pair from an LTS (Extended Data Fig. 4e). Notably, C predicted cross-reactive pWT, pMT and pMT, pMT substitutions in this neopeptide–TCR pair (Fig. 3f and Extended Data Fig. 5c, 6c). Thus, we combined all 1,197 TCR–pMT pairs to derive a composite C—the antigenic distance for a TCR to cross-react between amino-acid-substitution pairs (Fig. 3g and Extended Data Fig. 7c). Broadly, two factors promote cross-reactivity: substitutions at peptide termini27 and within amino acid biochemical families (driven by amino acids of similar size and hydrophobicity; Fig. 3g). With this composite C, we now define self-discrimination D between a pWT and its corresponding pMT (Fig. 3a) as

$$D({{bf{p}}}^{{rm{W}}{rm{T}}}to {{bf{p}}}^{{rm{M}}{rm{T}}})=(1-w)log ,left(frac{{K}_{{rm{d}}}^{{rm{W}}{rm{T}}}}{{K}_{{rm{d}}}^{{rm{M}}{rm{T}}}}right)+w,log ,left(frac{{{rm{E}}{rm{C}}}_{50}^{{rm{M}}{rm{T}}}}{{{rm{E}}{rm{C}}}_{50}^{{rm{W}}{rm{T}}}}right),$$

(1)

where (w) sets the relative weight between the two terms. We chose the parameters of the neoantigen quality model to maximize the log-rank test score of survival analysis on an independent cohort of 58 patients with PDAC5 (Supplementary Methods and Extended Data Table 1a).