O’Reilly3,14 & Vinod P. Balachandran1,2,3 ✉ Pancreatic ductal adenocarcinoma (PDAC) is lethal in 88% of patients1, yet harbours mutation-derived T cell neoantigens that are suitable for vaccines 2,3. Here in a phase I trial of adjuvant autogene cevumeran, an individualized neoantigen vaccine based on uridine mRNA–lipoplex nanoparticles, we synthesized mRNA neoantigen vaccines in real time from surgically resected PDAC tumours. After surgery, we sequentially administered atezolizumab (an anti-PD-L1 immunotherapy), autogene cevumeran (a maximum of 20 neoantigens per patient) and a modified version of a four-drug chemotherapy regimen (mFOLFIRINOX, comprising folinic acid, fluorouracil, irinotecan and oxaliplatin). The end points included vaccine-induced neoantigen-specific T cells by high- threshold assays, 18-month recurrence-free survival and oncologic feasibility. We treated 16 patients with atezolizumab and autogene cevumeran, then 15 patients with mFOLFIRINOX. Autogene cevumeran was administered within 3 days of benchmarked times, was tolerable and induced de novo high-magnitude neoantigen-specific T cells in 8 out of 16 patients, with half targeting more than one vaccine neoantigen. Using a new mathematical strategy to track T cell clones (CloneTrack) and functional assays, we found that vaccine-expanded T cells comprised up to 10% of all blood T cells, re-expanded with a vaccine booster and included long-lived polyfunctional neoantigen-specific effector CD8 + T cells. At 18-month median follow-up, patients with vaccine-expanded T cells (responders) had a longer median recurrence-free survival (not reached) compared with patients without vaccine-expanded T cells (non-responders; 13.4 months, P = 0.003). Differences in the immune fitness of the patients did not confound this correlation, as responders and non-responders mounted equivalent immunity to a concurrent unrelated mRNA vaccine against SARS-CoV-2. Thus, adjuvant atezolizumab, autogene cevumeran and mFOLFIRINOX induces substantial T cell activity that may correlate with delayed PDAC recurrence. PDAC is the third leading cause of cancer death in the United States4 and the seventh worldwide5. With an increasing incidence6, and a survival rate of 12%1 that has remained largely stagnant for nearly 60 years1, PDAC is projected to cause even greater global cancer deaths by 2025 (refs. 6,7). Surgery is the only curative treatment for PDAC. Yet, despite surgery, nearly 90% of patients have disease recurrence at a median of 7–9 months8,9, and the 5-year overall survival (OS) is only 8–10%8,9. Although adjuvant multiagent chemotherapies delay recurrence and are standard of care in surgically resected PDAC, nearly 80% of patients have disease recurrence at around 14 months4, and their 5-year OS is <30%10. Radiation, biologics and targeted therapies are also ineffective4. PDACs are almost completely insensitive (<5% response rate11,12) to immune checkpoint inhibitors. This insensitivity is partially attributed to the fact that PDACs have a low mutation rate that generates few neo - antigens12, mutation-generated proteins absent from healthy tissues that mark cancers as foreign to T cells, thus potenially rendering PDACs https://doi.org/10.1038/s41586-023-06063-y Received: 10 January 2023 Accepted: 6 April 2023 Published online: 10 May 2023 Open access Check for updates A list of affiliations appears at the end of the paper. Nature | Vol 618 | 1 June 2023 | 145weakly antigenic with few infiltrating T cells. However, recent observa - tions have shown that most PDACs in fact harbour more neoantigens2,3,13 than previously predicted14. Furthermore, studies of long-term survi- vors of PDAC2,3 have revealed that neoantigens may stimulate T cells in PDAC. Primary tumours enriched in immunogenic neoantigens also harbour around 12-fold higher densities of activated CD8+ T cells, which correlates with delayed disease recurrence and longer patient survival. Thus, as most PDACs harbour neoantigens with the poten - tial to stimulate T cells, strategies to deliver neoantigens may induce neoantigen-specific T cells and affect patient outcomes. Based on the observation that long-term survivors of PDAC mount spontaneous T cell responses against tumour-specific neoantigens not shared among patients2,3, we tested whether adjuvant individualized vaccines can stimulate neoantigen-specific T cells and provide clinical benefit in patients with surgically resected PDAC. Therapeutic mRNA vaccine technology has facilitated the rapid delivery of individualized neoantigen vaccines fully integrated into a routine oncologic work - flow15. Moreover, mRNA can be rapidly manufactured as individualized vaccines with multiple neoantigens16, can activate antigen-presenting cells17–20 and can be efficiently delivered using newly developed clinical-stage formulations21. Therefore, we hypothesized that an effec- tive individualized mRNA vaccine would induce neoantigen-specific T cells in PDAC, eliminate micrometastases and delay recurrence. To test this hypothesis, we conducted an investigator-initiated, phase I clinical trial of sequential adjuvant atezolizumab (Genentech), autogene cevumeran22, 23 (an individualized mRNA neoantigen vaccine containing up to 20 major histocompatibility complex class I (MHCI) and MHC class II (MHCII) restricted neoantigens in lipoplex nanoparti - cles intravenously delivered; Individualized NeoAntigen-Specific Ther - apy (iNeST), BioNTech and Genentech) and mFOLFIRINOX in patients with surgically resectable PDAC (Fig. 1a) to : (1) amplify neoantigen- specific T cells inhibited by PD-1 signalling; and (2) prime naive T cells to vaccine neoantigens. Safety, feasibility and immunogenicity From December 2019 to August 2021, we enrolled 34 patients, of which 28 patients (Fig. 1b) underwent surgery. We then treated 19 patients with atezolizumab, of which 16 patients received subsequent autogene cevumeran. Fifteen out of these 16 patients also received subsequent mFOLFIRINOX (Fig. 1b). We analysed safety in a safety-evaluable cohort (n = 19 patients treated with atezolizumab, n = 16 treated with autogene cevumeran), and we correlated immune response to RFS in a biomarker-evaluable cohort (n = 16 patients treated with atezolizumab and autogene cevumeran). All 19 evaluable participants had clinical characteristics typical of patients with resectable PDAC (Extended Data Fig. 1a). All patients were treated and followed at the Memorial Sloan Ket - tering Cancer Center (MSK) during and beyond the enrolment period. None of the 19 patients treated with atezolizumab in the safety- evaluable cohort had grade 3 or higher adverse events (AEs; Fig. 1c ). One out of 16 (6%) patients treated with autogene cevumeran in the safety-evaluable cohort had grade 3 AEs (fever and hypertension; Fig. 1c). All 16 patients (100%) who received autogene cevumeran had grade 1–2 AEs (Extended Data Fig. 1c). We administered atezolizumab and autogene cevumeran at median times within 1 and 3 days of respec - tive benchmarked times (median time to atezolizumab was 6.1 weeks (range of 4.3–7.9 weeks); median time to autogene cevumeran was 9.4 weeks (range of 7.4–11.0 weeks); Fig. 1d). Only 1 patient out of 19 (5%) had insufficient neoantigens that led to non-manufacture of the vac - cine (Fig. 1b). Three out of 16 patients (19%) did not receive all 9 vaccine doses (Fig. 1d), which was due to progression, death or mFOLFIRINOX toxicity. Thus, autogene cevumeran can be rapidly administered even after complex oncologic surgery. Next, to measure the T cell responses induced by autogene cevu - meran, we utilized a previously described ex vivo IFNγ ELISpot assay24 that detects high-magnitude T cell responses to vaccines without dis - tinguishing CD8+ from CD4+ T cell responses. Eight out of 16 (50%) patients who received the vaccine generated T cell responses that were detected by ex vivo IFNγ ELISpot, and were deemed autogene cevu - meran responders (Fig. 1e). By testing each specific target included in the neoantigen vaccines, we detected that 25 out of the 230 neoanti - gens (11%) administered across all patients who were evaluable at the single-target level induced a T cell response of sufficient high magni- tude to be detectable by ex vivo IFNγ ELISpot (Fig. 1e and Extended Data Fig. 2a). Half of all the patients who received the vaccine mounted neoantigen-specific T cell responses against at least one vaccine neo - antigen (median = 2, range = 1–8; Extended Data Fig. 2b). Furthermore, half of these responses were polytopic, targeting more than one vac - cine neoantigen (Fig. 1e,f ). No T cell responses against vaccine neo - antigens were detectable before vaccination by ex vivo IFNγ ELISpot (Fig. 1f ). Neoantigen-specific immune responses after vaccination were detected at levels that ranged from approximately 100 spots per million bulk peripheral blood mononuclear cells (PBMCs) to >2,000 spots per million bulk PBMCs (Fig. 1g ). Inter-patient variation in the number and magnitude of all responses and intra-patient variation in the magnitude of polytopic responses were observed (Fig. 1g). Thus, autogene cevumeran induces substantial de novo T cell responses in a large proportion of patients with PDAC. T cell clonotypes and phenotypes To confirm ELISpot assay reactivity using an orthogonal technique and to probe the diversity and specificity of autogene-cevumeran-expanded T cell clones, we developed CloneTrack. CloneTrack is a new math - ematical and immunological method that uses T cell receptor (TCR) Vβ sequencing of peripheral blood samples before and after treat - ment to identify treatment-expanded high-magnitude T cell clones (Methods). Using CloneTrack, we detected vaccine-induced clonal expansion in 8 out of 8 responders and in 1 out of 8 non-responders (Fig. 2a,b and Extended Data Fig. 2d). In responders, autogene cevu - meran expanded multiple clones (median of 7.5 clones; Fig. 2c ) from undetectable levels to up to 10% (median of 2.8%; Fig. 2c) of all blood T cells. Analogously, we applied CloneTrack to peripheral blood sam- ples collected before and after atezolizumab treatment and found that autogene-cevumeran-expanded T cell clones did not overlap with atezolizumab-expanded T cell clones (Extended Data Fig. 3a–c). To assess the antigen specificity of autogene-cevumeran-expanded T cell clones, we identified T cell clones specific to ELISpot-identified immu - nodominant neoantigens in vitro and examined the clonal overlap to autogene-cevumeran-expanded clones in vivo in 2 patients with mono - topic responses and in 2 patients with polytopic responses (Fig. 2d and Extended Data Fig. 4a,b). Three out of 4 patients (75%) and 51% (n = 21 out of 41 clones) of vaccine-expanded high-magnitude clones (28 out of 41 clones detected in 1 patient) contained immunodominant neoantigen-specific clones (Fig. 2e). In the fourth patient (patient 11), the immunodominant neoantigen-specific clones were in a lower mag - nitude vaccine-expanded clonal pool (Extended Data Fig. 4b). Thus, autogene cevumeran expands de novo polyclonal neoantigen-specific T cells in PDAC. We next studied the phenotype and function of autogene- cevumeran-expanded T cells. Using single-cell RNA sequencing, we found that autogene-cevumeran-expanded high-magnitude clones were CD8+ T cells that expressed lytic markers (perforin 1 and gran - zyme B) and cytokines (IFNγ) and resembled effector T cells induced by protective viral vaccines25 (Fig. 2f and Extended Data Fig. 5a–c). Consistently, peripheral blood samples collected after vaccination con - tained polyfunctional CD8+ T cells but not CD4+ T cells that produced cytokines (IFNγ and TNF) and degranulated on in vitro rechallenge with both long neopeptides (Fig. 2g and Extended Data Fig. 5d) and MHCI-restricted minimal epitopes (Fig. 2h and Extended Data Fig. 5e). 146 | Nature | Vol 618 | 1 June 2023 ArticleNotably, autogene-cevumeran-expanded T cells maintained functional - ity despite post-vaccination mFOLFIRINOX treatment, with persistent IFNγ production (Fig. 1f), uniform re-expansion with a vaccine booster in all responders (Fig. 2i) and sustained persistence as high as 2.5% of all blood T cells up to 2 years after surgery (Fig. 2c and Supplementary Table 1). Furthermore, vaccine boosters re-expanded identical primed clones in 7 out of 7 patients who received boosters (47% of all primed clones; Fig. 2i and Extended Data Fig. 6). Although autogene cevumeran expanded multiple clones, standard flow cytometry did not reliably detect T cell expansion and activation (Extended Data Fig. 5f). Collec- tively, autogene cevumeran substantially expanded T cells that included vaccine neoantigen-specific, functional and durable CD8+ T cells. Vaccine response and clinical outcome At a median follow-up of 18 months that extended beyond the prespeci - fied secondary end point, the median OS and RFS of the patients in the safety-evaluable cohort were not reached (Fig. 3a). For patients in the biomarker-evaluable cohort, the 8 autogene cevumeran responders had a median RFS that was not reached compared with the 8 non- responders who had a median RFS of 13.4 months (P = 0.003, hazard ratio (HR) = 0.08 (95% confidence interval (CI) 0.01–0.4); Fig. 3b). To exclude a time-to-response bias26, we performed a landmark analysis to correlate RFS to response in patients who were recurrence-free when completing all 8 autogene cevumeran priming doses (landmark RFS). The median landmark RFS was similarly not reached in responders com - pared with 11.0 months in non-responders (P = 0.008, HR = 0.06 (95% CI 0.008–0.40); Fig. 3b). Consistently, compared with non-responders, responders had persistently lower serum CA19-9 levels (Extended Data Fig. 7a), the most widely used clinical PDAC biomarker27. Only 25% of patients in the biomarker-evaluable cohort had detectable circulat - ing tumour DNA at diagnosis (Extended Data Fig. 7b), as previously reported in patients with resectable PDAC tumours28,29, and thus was not a reliable biomarker of recurrence. To identify if responders were a b 02040 AnyFeverHyper-tensiond Autogene cevumeranAny Atezolizumab–501 P = 0.03Autogene cevumeran (n = 15)* Benchmark AchievedDifferenceAtezolizumab (n = 18)*Autogene cevumeran (n = 16) –50–1 Difference between means036912 Doses 036912 –501Weeks afer surgery5 ResectionProcess and transport tissuesPredict and select neoantigensCustom manufacture autogene cevumeran (individualized neoantigen-encoding mRNA–lipoplex)Sequence tumour and normal DNA Tumour RNA Week 0 Screen for eligibility69 Atezolizumab 1 doseSurgeryAutogene cevumeran 21 Priming doses 1–8Follow-up 12 cycles (biweekly)43 17 46 Booster dose 9 80100 60Grade 3 AEs (%)cmFOLFIRINOXKey inclusion criteria • All surgically resectable PDAC - No borderline resectable - No locally advanced or metastatic disease - No neoadjuvant therapy • ≥5 neoantigens e +Neopeptides (15-mer) or controlsPBMCs Before vaccineAfter priming Neoantigen 1 Positive controlNegative control50% 50% Responders (n = 8) Non-responders(n = 8)Responders (n = 8) MonotopePolytope50% 50%f g Patient1029251156141IFN/uni03B3+spots per 106 cells 01002003004005001,5003,000Responders (n = 8)Non-responders (n = 8)Number of neoantigens in autogenecevumeran Patient:05101520 10 25 6 11 141194 18 2092328 29 5 3 Immunogenic Non-immunogenic No dataR0/R1:R0R0R0 R0R0R0 R0R0R0 R0R0R0 R0 R1 R1 R134 screened and consented 2 excluded •2 did not meet inclusion criteria 32 enrolled 28 resected on protocol4 removed before resection •3 withdrew consent •1 had disease progression 19 received atezolizumaba 16 received vaccineb 15 received mFOLFIRINOX9 removed before atezolizumab •6 advanced or metastatic diseas e 1 non-PDAC diagnosis 1 withdrew consent1 manufacture failure (inadequate tissue) • • • 3 removed before vaccine •1 disease progression 1 for other cancer treatment1 insufficient neoantigens• • 1 removed before mFOLFIRINOXEvaluable patients•1 disease progression aSafety-evaluable cohort bBiomarker-evaluable cohort 100101102103104 Patient 1 5 6 10 11 14 25 29<10–4 0.002IFN/uni03B3+spots per 106 cells 0P:Benchmark Achieved Difference BenchmarkAchieved Difference036912Weeks afer surgery Difference between meansDifference between means Vaccinepriming Chemo&XVWRPPDQXIDFWXUH DXWRJHQHFHYXPHUDQ Fig. 1 | Individualized mRNA neoantigen vaccines are safe, feasible and immunogenic in patients with PDAC. a,b, Trial design ( a) and consolidated standards of reporting trials diagram ( b). c, Percentage of grade 3 AEs attributable to atezolizumab and autogene cevumeran (vaccine) in atezolizumab ( n = 19) and vaccine ( n = 16) safety-evaluable patients. Blue line indicates the study-defined safety threshold (25%). d, Achieved and benchmarked times to atezolizumab (left) and first vaccine dose (middle), and number of vaccine doses (right). Red line indicates the median, error bars are 95% confidence intervals and dotted lines the zone of clinical indifference. Asterisks indicate patients on study- specified treatment sequence. e–g, PBMCs collected after atezolizumab and before vaccine administration, 1–3 weeks after vaccine priming, and 5–6 weeks after mFOLFIRINOX were analysed for IFNγ + T cells specific to all individual vaccine neoantigens by ex vivo IFNγ ELISpot in n = 16 patients in the biomarker- evaluable cohort. Patients were classified as responders if ELISpot detected IFNγ+ T cell induction against at least one vaccine neoantigen. e , Left, schematic and representative image of ex vivo IFNγ ELISpot. Middle, Number of vaccine neoantigens per patient that induced IFNγ+ T cells in PBMCs collected after vaccine priming. R0/R1 indicates the surgical margin status. For patient 25, 2 out of 5 ELISpot responses were detected against 2 neoantigen pools (pool 1 with 2 neoantigens, pool 2 with 5 neoantigens). Right, Proportion of vaccine responders and non-responders. f ,g, Normalized ex vivo IFNγ ELISpot counts for vaccine neoantigens that induced a de novo response ( n = 25 neoantigens in 8 patients): longitudinal ( f, left); after priming ( g). Spot counts of the non-stimulated controls were subtracted. Proportion of patients with monotope compared with polytope responses to all vaccine neoantigens ( f, right). n indicates individual patients. Chemo, chemotherapy (mFOLFIRINOX). P values calculated using two-tailed unpaired t -test ( d) or Wilcoxon matched-pairs signed-rank test ( f). Nature | Vol 618 | 1 June 2023 | 147b Non-responders (n = 8) Atezolizumab Autogene cevumeran mFOLFIRINOX Surgery02 0 80 40 60 Weeks after surgery1000.0010.010.1110100 02 08 0 40 60 100aResponders (n = 8) Patient: n = 28 clonesPercentage of all blood T cells0.0010.010.11101001 Total Mean n = 2 clones56 n = 7 clones10 n = 9 clones11 25 29 n = 2 clones n = 6 clones n = 15 clones n = 10 clones14 Adjusted P for de novo expansion11 0–610–210–40208 0 4060 Weeks after surgery1000208 0 4060 1000208 0 4060 1000208 0 4060 1000208 0 4060 1000208 0 4060 1000208 0 4060 1000208 0 4060 100Atezolizumab Autogene cevumeran mFOLFIRINOX SurgeryIFN /uni03B3+ spots per 106 cells 1101001,00010,000Clones: NA speci/f_icity: n = 16 clones n = 12 unidenti/f_ied n = 2 clones n = 3 clonesn = 6 unidenti/f_ied n = 2 unidenti/f_ied ** ** *Not tested 050100 Patients (%) ELISpot: +–CloneTrack+ CloneTrack– 8 8 n =P < 10-4 0102030T cell clones (number) Before AfterP = 0.03 Median 2.8 Vaccine:0.0010.010.110 1 0.0001c d 4-1BBCD8TCR1 TCR6 TCR10T CR11 TCR12T CR14 KLQLACRLQKVAAL (HLA-A*32:01) 54.1 38.0 55.2 45.9 57.8 64.8 2.3 2.7 1.6 3.9 1.6 2.6 1.4 1.1 0.5 2.9 1.1 1.5 0.9 2.1 0.4 1.3 1.2 0.6 KVAALVENKVTDL (HLA-A*32:01)CRLQKVAALV (HLA-C*07:01)RLQKVAAL (HLA-A*32:01)Control 12 16 4Vaccine expandedNeoantigen speci/f_icIn vitro vaccine neoantigen-speci/f_ic T cell activation 100102104CD107a+ CD107a–100102104Neopeptide pool Neopeptide pool speci/f_icity (P)11 0–310–6100102104IFN/uni03B3 ELISpot 02 08 0 40 60 100IFN/uni03B3+ spots per 106 cells 1101001,00010,000 Neopeptide pool Weeks after surgeryNeopeptide poolTCR cloning Total frequency Mean n = 28 clones 0.0010.010.1110100 02 08 0 40 60 Weeks after surgery100 Adjusted P for de novo expansion11 0–610–210–4 Atezolizumab Autogene cevumeran mFOLFIRINOXSurgeryT cell clonal expansion by CloneTrack Effector:target ratio = 1: 5 UMAP1UMAP2 Dysfunctional EffectorMemory NaivePhenotype UMAP1PRF1 (perforin 1) GZMB (granzyme B) UMAP1 UMAP 01.02.03.0 Patient 1 1 10 11 29UMAP1Vaccine-expanded CD8+ T cellsCD8+ T cells Before priming After boost Expressionf Control Neopeptide poolg Control Neopeptide pool0.1110100(IFN/uni03B3 and/or TNF)+ (%) CD107+ (%)P = 0.03e Present Absentn = 4 patients25% 75% IFNG (IFN/uni03B3) 01.02.0 1.5 0.5 Expression Control NeopeptidepoolCD8+ P = 0.03Neoantigen speci/f_ic Unidenti/f_iedn = 41 clones49%5 1%0.0001 Patient 1 5 6 10 11 14* 25 29 *0.0001Responders (n = 8) Patient 3* 4* 9 18* 19 20 23 28 ** ** IFN/uni03B3 TNFCD4CD8 0.3 18.2 0.3 0.2P = 0.03CD8+CD4+(IFN/uni03B3 and/or TNF)+ (%) 0.1110100 Control NeopeptidepoolControl Neopeptidepool CD107aCD8Control Neopeptide poolIFN/uni03B3 TNF 67.1 0.2 1.2 64.1h CD8+ i n = 5 neoantigens from 5 patientsNon- responders (n = 8) Percentage of all blood T cells 0.0010.010.110Responders (n = 8) 1 0.0001Non-responders (n = 1) 0.0080.020.02 P: n = 77 clones 47%22% 31% Expanded Non-expanded UndetectableBoost:Responders with booster (n = 7) n = 5 neoantigens from 4 patients Percentage of all blood T cellsPercentage of all blood T cells Percentage of all blood T cellsWeeks after surgeryResponders (n = 8) CD107a– Vaccine priming Chemo Vaccine booster Vaccine priming Chemo Vaccine booster01 02 03 04 05 06 07 08 09 0100 1102551 Weeks after surgeryPatient2.55 0.03 0.47 0.21 2.64 4.09 0.0382 100 0.18 10080 86 93 100 50Atezolizumab Autogene cevumeranmFOLFIRINOX 1129614 10 *At/f_inal assessment Percentage of all blood T cellsPercentage of persisting clones Fig. 2 | mRNA vaccines expand polyclonal, polyfunctional effector CD8+ T cells. a, Vaccine-expanded T cell clones assessed using CloneTrack (top), vaccine-induced IFNγ by ELISpot (bottom) and their correlation (right). b,c, Vaccine-expanded clones identified by CloneTrack: longitudinal aggregate percentage ( b), number of unique clones ( c, left), before vaccine and peak expansion aggregate percentage ( c, middle), and final per patient assessment times (bar graph) with aggregate percentage and clonal fraction at final assessment ( c, right). For b , inverted triangles indicate collection times for single-cell sequencing in f and circles indicate vaccine booster. d, Immunodominant vaccine neoantigen-specific clonal overlap with vaccine- expanded clones and specificity to immunodominant vaccine-neoantigens by TCR cloning in patient 1. e , Left, Percentage of patients with immunodominant vaccine neoantigen-specific clones in vaccine-expanded clones. Right, Percentage of vaccine-expanded clones specific to immunodominant vaccine neoantigens. f, Single-cell phenotypes of vaccine-expanded CD8 + T cells. Dots indicate blood CD8+ T cells. Coloured dots (far left) indicate vaccine-expanded clones in a . g,h, Percentage of IFNγ+, TNF+ and CD107a+CD8+ (g,h) and CD4+ T cells ( g) in PBMCs after vaccine priming with ex vivo immunodominant long ( g) or minimal ( h) neopeptide rechallenge. Representative flow plots from patient 1 ( g, h ). Pregated on CD3+CD56–CD8+ (g,h) or CD4+ (g) cells. i, Left, Aggregate percentage of vaccine-expanded clones with priming, chemotherapy and booster in peripheral blood. Right, Percentage of primed clones that re-expand with booster. n indicates individual clones or patients. In a and d, the green lines indicate individual clone trajectories; the black line, the geometric mean clonal trajectory (error bars are the geometric s.d.); the red line, the cumulative percentage of all expanded clones. In b,c, asterisks indicate altered treatment schedules. In b–d , rectangles indicate the treatment sequence. P values calculated using modified two-tailed Fisher’s exact test (a,d, left), two-sided Chi square test ( a, right), two-tailed paired t-test (c), one-tailed binomial test with Bonferroni correction ( d, middle) or two-tailed Wilcoxon matched-pairs signed-rank test ( g–i). 148 | Nature | Vol 618 | 1 June 2023 Articlemerely enriched in patients with better prognosis, we found response to atezolizumab, lymph node positivity, margin positivity, primary tumour size, the number of chemotherapy doses and density of intratumoural CD8+ T cells did not correlate with vaccine response (Extended Data Figs. 1b and 7c–e). Responders and non-responders also had comparable immunological fitness, as they mounted equiva - lent humoral and cellular responses to an unrelated mRNA vaccine (SARS-CoV-2) that was concurrently administered with autogene cevumeran (Extended Data Fig. 8). Responders and non-responders also had equivalent peripheral frequencies of all major innate and adaptive immune cells (Extended Data Fig. 9a–c), and similar somatic and germline genetic characteristics (Supplementary Tables 2–4). In summary, the autogene-cevumeran-expanded T cell response cor- relates with delayed PDAC recurrence that is not confounded by detect - able differences in patient selection, intratumoural T cell frequency or peripheral T cell frequency or fitness. As autogene cevumeran induced high-magnitude T cell responses specific to 25 out of 106 vaccine-encoded neoantigens (24%) in respond - ers (Extended Data Fig. 2a), we searched for correlates of vaccine response. Our previous findings2,3,30 showed that CD8+ T-cell-enriched PDAC tumours are also enriched in immunogenic ‘high-quality’ neo - antigens distributed in greater proportions across tumour clones. Therefore, we examined whether tumour clonality and neoantigen quality correlate with vaccine-induced T cell responses. Consistently, responders to autogene cevumeran had more clonal tumours than non-responders (Extended Data Fig. 10a). Next, we examined whether immunogenic neoantigens in responders contained high-quality fea- tures. We adapted our previously described model2,3 (Methods) that identifies spontaneously targeted neoantigens in tumours to cor - relate immunogenicity to the quality of vaccinated neoantigens. In responders, neoantigen quality as a continuous variable correlated with vaccine neoantigens that induced IFNγ ELISpot responses (Extended Data Fig. 10b). Notably, non-responders had similar numbers of non-synonymous mutations and vaccine neoantigens as responders (Extended Data Fig. 2c). Vaccine clones and a micrometastasis Patient 29 responded to autogene cevumeran with the second- highest maximal percentage of expanded blood T cells (Fig. 2b) that included vaccine neoantigen-specific polyfunctional CD8+ T cells (Extended Data Fig. 5d,e). Patient 29 developed increased serum CA19-9 levels with a new 7-mm liver lesion suggestive of a metastasis after vaccine priming (Fig. 4a). A biopsy sample did not reveal malignant cells but a dense lymphoid infiltrate (Fig. 4b , left) that included all 15 autogene-cevumeran-expanded (Fig. 4b , middle) CD8+ T cell clones with phenotypic evidence of lytic and effector potential (Fig. 4d). Digital droplet PCR revealed that this lymphoid infiltrate contained rare cells harbouring the TP53R175H mutation, identical to the R175H driver muta - tion in the primary tumour of this patient (Fig. 4c and Extended Data Fig.