Neoantigen quality predicts immunoediting in survivors of pancreatic cancer

1In 1957, Burnet and Thomas proposed that the immune system in multicellular organisms must eliminate transformed cells as an evolutionary necessity to maintain tissue homeostasis. This theory of ‘cancer immunosurveillance’ was later redefined more broadly as ‘cancer immunoediting’—as a consequence of the immune system protecting the host from cancer, the immune system must also sculpt developing cancers,. When cancers develop, they accumulate mutations, some of which generate new protein sequences (neoantigens). As neoantigens are mostly absent from the human proteome, they can escape T cell central tolerance in the thymus to become antigens in cancers. However, neoantigens typically arise in passenger mutations, and therefore distribute heterogeneously in cancer cell clones with variable immunogenicity. Thus, T cells selectively ‘edit’ clones with more immunogenic neoantigens, inducing less immunogenic clones to outgrow in cancers.

2Although cancer immunoediting has been demonstrated through longitudinal studies in immune-proficient and immune-deficient mice,,, whether it is a general principle of how human cancers evolve remains uncertain. Despite suggestive evidence–, definitive evidence requires longitudinal tracking of large numbers of patients and cancers over time. As this is logistically challenging, whether the human immune system naturally edits cancers and whether edited clones can be predicted a priori remain unclear.

3To address this, we examined how 70 pancreatic ductal adenocarcinomas (PDACs) from 15 patients evolved longitudinally over 10 years (Fig. 1a). We reasoned that PDAC is an ideal cancer to test the immunoediting hypothesis. First, human PDACs have fewer neoantigens (35 on average), compared with more immunogenic cancers (112 in non-small-cell lung cancer, 370 in melanoma on average). This theoretically maximizes our ability to both distinguish true neoantigen selection from neutral genomic changes over time and isolate effects of individual neoantigens on clonal selection. Second, T cell infiltrates in PDACs range from nearly zero to 1,000-fold higher. Thus, PDACs have subsets that approximate immune-deficient and immune-proficient cancers, enabling us to theoretically observe how differential immune selection pressures modulate cancer cell clones. Finally, mutations in oncogenes occur early in PDAC carcinogenesis and are clonal—this largely equalizes the cell-intrinsic oncogenic pressures among clones, maximizing our ability to detect how cell-extrinsic immune pressures affect clonal evolution.

4To model how immune-proficient and immune-deficient human cancers evolve, we compared how primary PDACs evolve to recurrence in a cohort of long-term survivors (LTSs) and short-term survivors (STSs) (Fig. 1a, b and Supplementary Table 1). We previously demonstrated that, compared with STSs, LTSs have primary tumours with around a 12-fold greater number of activated CD8+ T cells,, that are predicted to target immunogenic neoantigens, therefore phenocopying relative greater immune pressure. Furthermore, in the current cohort we find that the largest T cell clones of LTS tumours have more similar CDR3β sequences compared with the largest T cell clones in STS tumours (Extended Data Fig. 1a, b), suggesting T cell clonal expansion and therefore greater immune activity in LTSs. We therefore hypothesized that this higher immune pressure in LTSs would induce tumours to preferentially lose tumour clones with immunogenic neoantigens over time (Fig. 1a). To test this hypothesis, we compared how tumours evolved from primary to recurrent tumours. We found that compared with STSs, LTSs had later (Fig. 1c) and fewer recurrent tumours (Fig. 1d) that inversely correlated with longer survival times (Fig. 1e). Moreover, 75% of LTSs versus 0% of STSs had recurrent tumours that were only metastatic (Fig. 1f), with distinct tissue-tropic recurrence patterns (Fig. 1g). Thus, LTS tumours recur with distinct latency, multiplicity and tissue-dependent evolutionary trajectories.

5To examine whether differential selection pressure could explain these unique recurrence patterns, we performed whole-exome sequencing (Extended Data Fig. 2a) and inferred the clonal structures of matched primary and recurrent tumours. We reasoned that greater immune selection pressure in LTS tumours should limit the diversity of tumour clones over time, due to immunoediting of neoantigens. Consistently, we found that, although primary tumours in LTSs were only slightly more homogeneous than in STSs, recurrent tumours in LTSs were much more homogeneous (Fig. 2a (left)), indicating that LTSs probably evolved fewer clones (Fig. 2a (right) and Extended Data Fig. 3a, b). To examine whether this could be explained by greater selection pressure on neoantigens, we compared the total number of non-synonymous mutations (tumour mutational burden (TMB)) and computationally predicted MHC-I restricted neoantigens,. Consistently, although primary LTS tumours had a similar TMB with a comparable number of neoantigens as STS tumours (Fig. 2b), recurrent LTS tumours had a lower TMB with fewer neoantigens (Fig. 2b). Despite these differences, LTS and STS tumours had comparable numbers of synonymous mutations and mutations in driver oncogenes (Extended Data Fig. 2b, c). Although recurrent tumours of LTSs had fewer co-occurring mutations in oncogenes compared with recurrent tumours of STSs (Extended Data Fig. 2d), the number of mutations in oncogenes did not correlate with TMB (Extended Data Fig. 2e). Furthermore, LTS recurrent tumours gained significantly fewer mutations and neoantigens compared with STS recurrent tumours (Fig. 2c), remaining largely neutral over time. LTS tumours also gained fewer mutations that generate neoantigens than STS tumours (Fig. 2d), indicating that LTS tumours preferentially depleted neoantigenic mutations. These data support the hypothesis that greater immune selection in LTS tumours edited tumour clones and neoantigens.

6To identify the edited neoantigens, we extended our previous neoantigen quality model, 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.

7By 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, previously introduced as the MHC amplitude A (refs.,), 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, 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 ). 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.

8To model C, we leveraged recent findings that conserved structural features underlie TCR–peptide recognition. Specifically, the binding domains of peptide-degenerate TCRs, and TCR-degenerate peptides 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 cytomegalovirus that was previously used to model TCR–peptide degeneracy, 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 gp100, (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. 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 termini 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) aswhere 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 PDAC (Supplementary Methods and Extended Data Table 1a).

9We applied our model to PDAC, positing that immunoediting will differentially deplete neoantigens with higher D (less self) in LTS versus STS PDACs. First, we stratified the frequency of mutations by the antigenic distance as defined by C (Fig. 3g and Supplementary Methods). Compared with mutations with a lower antigenic distance, mutations with a greater antigenic distance from self were more significantly depleted in both LTS and STS PDACs (Fig. 3h (left and middle)) and, interestingly, preferentially more depleted in LTS compared with STS PDACs (Fig. 3h (right)). To further examine these observations, we applied the full D model to find that neoantigens with both a higher C and D were strikingly more depleted in LTS versus STS PDACs (Fig. 3i). Interestingly, genes in the HLA class-I pathway were not differentially mutated, deleted, expressed or localized in STS versus LTS PDACs, indicating that neoantigen depletion was not accompanied by acquired resistance in the HLA class-I pathway in LTSs (Extended Data Fig. 8a–c). Thus, tumours in LTSs selectively lose high-quality neoantigens.

10We next incorporated neoantigen quality parameters into a fitness model, to test whether our model that predicts clonal tumour evolution can identify immunoedited clones. We reconstructed joint multisample phylogenies for all tumours from each patient to provide a common clonal structure and track clone frequencies between the tumours of the same patient. To describe selective pressures acting on tumour clones, we accounted for positive selection due to cumulative mutations in driver oncogenes. We quantify this effect in a minimal model, which counts the number of missense mutations in canonical PDAC driver genes (KRAS, TP53, CDKN2A and SMAD4) in each clone α. The composite fitness model (Fig. 4a) defines fitness function, Fα, of clone α as the sum of a negative fitness cost due to immune recognition of high-quality neoantigens and positive fitness gain due to the accumulation of mutations in driver oncogenes,

11with the free parameters σI and σP setting the amplitude of the fitness components (Supplementary Methods). We use the model to predict the frequencies of clones propagated to recurrent tumours aswhere is the frequency of clone α in the primary tumour, is its predicted frequency in the recurrent tumour and constant Z ensures correct normalization. We evaluated how closely the fitness model predicted clonal evolution in the recurrent tumours. To do this, for each recurrent tumour in the LTS and STS cohorts, we performed maximum-likelihood fitting of the model parameters σI and σP in equation (3).

12We found that our model provided a better fit of the observed evolution of LTS compared to STS tumour clones, predicting observed evolution in 86% of LTS tumours versus 52% of STS tumours (Extended Data Table 1b) when compared with a neutral model (no selection pressure on clones; differences were quantified with a Bayesian information criterion; Supplementary Methods). Notably, a partial fitness model that incorporates only the oncogenicity component,, showed reduced performance for the LTS tumours but not STS tumours (Extended Data Table 1b and Extended Data Fig. 9). To illustrate this further, we compared observed and model-fitted clone frequency changes between the primary and recurrent tumours, and (Fig. 4b), for all reliably predictable clones in the primary tumour (above 3% frequency; Supplementary Methods). The direction of frequency changes was correctly predicted for 71% of LTS and 58% of STS tumour clones (rank correlation ρ of 0.65 and 0.28, respectively; Fig. 4b and Extended Data Table 1b). We attribute the model’s better predictions in LTS tumours to the presence of immune selection in these tumours.

13Next, we computed the overall tumour immune cost (averaging the immune component, over all tumour clones). Consistently, the immune fitness cost was lower in recurrent LTS tumours compared with in STS tumours (Fig. 4c). Furthermore, we considered the immune cost only of clones that are new in recurrent tumours, but not present in primary tumours. Recurrent LTS tumours contained both fewer new neoantigens (1% versus 18%; Fig. 4d) and new clones with markedly lower immune fitness cost (Fig. 4e) compared with recurrent STS tumours. These observations again suggest that the LTS recurrent tumours had been subject to immunoediting.

14Finally, we confirmed these results by analysing TCR sequencing data in the available recurrent tumour samples. We quantified the specificity of T cell clonal expansion using the TCR dissimilarity index (Supplementary Methods and Extended Data Fig. 1a, b) and correlated this index to immune fitness cost. We found greater T cell clonal expansion in tumours (lower TCR dissimilarity index) correlated with more highly edited tumours (lower immune fitness cost) (Fig. 4f and Extended Data Fig. 1c). In summary, these results strongly suggest that neoantigens are immunoedited in PDAC, and that our fitness model captures the selective pressures by T cells acting on tumour clones.

15Here we clarify several questions on how the immune system interacts with cancer. First, does cancer immunoediting occur in humans? As the theory of cancer immunoediting was developed by studying carcinogen-induced highly mutated murine sarcomas,, it has remained uncertain whether these principles apply to human cancers–. We postulated that spontaneous immunoediting of a human cancer should manifest when the immune system recognizes an immunogenic antigen in a primary tumour, as this should induce the antigen to be subsequently eliminated in the recurrent tumour. Indeed, this is what we found—tumours that evolve under stronger immune pressure lose more immunogenic neoantigens. Although we did not assess the changes in non-mutated antigens or address how different cellular compositions and tissue environments may modulate editing, it is notable that the proof for immunoediting is revealed in PDAC, a low-mutated cancer that is considered to be resistant to endogenous immunity. This strengthens the claim that immunoediting is a broadly conserved principle of carcinogenesis.

16Second, does immunoediting manifest as loss of immunogenic antigens, or do cancers also acquire genetic resistance? Interestingly, we observed the former but not the latter. We postulate that such phenotypes are governed by the magnitude of the selective pressure. Although LTSs exhibit higher immune pressures in tumours than STSs, this is ostensibly still lower than pharmacologically boosted immune pressure in a tumour. Thus, in LTSs, as pressure is moderate, tumours lose immunogenic antigens; by contrast, where pressure is maximal, such as perhaps when under therapy, tumours acquire resistance. This distils cancer evolution under immune selection to a simpler concept—selection determines clonal composition, and pressure determines adaptive change. Further studies will test these concepts.

17Third, can we quantify how the immune system recognizes mutations? We combined experimental techniques and machine learning to present a new metric that captures how T cells cross-react between peptides. We use C to quantify the antigenic distance of mutated peptides in the TCR-recognition space and the qualities that render individual mutations immunogenic, building on our previous efforts, to formalize antigen quality. Although we used our quality model to identify immunogenic neoantigens, we propose that it captures common immunogenic features in antigens. Thus, we anticipate that our model can further illuminate the biology of antigens beyond cancer, including T cell cross-reactivity between antigens, pathologies of cross-reactivity (such as autoimmunity) and therapies that require rational antigen selection (such as vaccines).

18Finally, it is notable that quantifying the ability of the immune system to discriminate changes in mere single amino acids can predict how cancers evolve. This undoubtedly reflects that a fundamental function of the immune system is to maintain integrity of the host genome. We therefore speculate that our model in essence captures the mechanisms through which the immune system preserves genomic integrity.

19Further information on research design is available in the Nature Research Reporting Summary linked to this paper.

20Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41586-022-04735-9.