Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer methods
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After surgery, we included patients with pathologically confirmed PDAC with R0/R1 margins. Additional eligibility criteria and ethical study conduct information are in the protocol (Supplementary Data ). We aimed to accrue 20 evaluable patients.
Surgery
Patients underwent open pancreaticoduodenectomy or either open or laparoscopic distal pancreatectomy and splenectomy at MSK. We then transported tumour blocks with the most (minimum ≥10%) histological tumour content with matched blood to BioNTech.
Main
PDAC is the third leading cause of cancer death in the United States and the seventh worldwide. With an increasing incidence, and a survival rate of 12% that has remained largely stagnant for nearly 60 years, PDAC is projected to cause even greater global cancer deaths by 2025 (refs., ). Surgery is the only curative treatment for PDAC. Yet, despite surgery, nearly 90% of patients have disease recurrence at a median of 7-9 months,, and the 5-year overall survival (OS) is only 8-10%,. 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 months, and their 5-year OS is <30%. Radiation, biologics and targeted therapies are also ineffective.
Main
To test this hypothesis, we conducted an investigator-initiated, phase I clinical trial of sequential adjuvant atezolizumab (Genentech), autogene cevumeran, (an individualized mRNA neoantigen vaccine containing up to 20 major histocompatibility complex class I (MHCI) and MHC class II (MHCII) restricted neoantigens in lipoplex nanoparticles intravenously delivered; Individualized NeoAntigen-Specific Therapy (iNeST), BioNTech and Genentech) and mFOLFIRINOX in patients with surgically resectable PDAC (Fig. ) to: (1) amplify neoantigen-specific T cells inhibited by PD-1 signalling; and (2) prime naive T cells to vaccine neoantigens. 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...
Safety, feasibility and immunogenicity
From December 2019 to August 2021, we enrolled 34 patients, of which 28 patients (Fig. ) 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. ). 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. ). All patients were treated and followed at the Memorial Sloan Kettering Cancer Center (MSK) during and beyond the enrolment period.
Safety, feasibility and immunogenicity
None of the 19 patients treated with atezolizumab in the safety-evaluable cohort had grade 3 or higher adverse events (AEs; Fig. ). One out of 16 (6%) patients treated with autogene cevumeran in the safety-evaluable cohort had grade 3 AEs (fever and hypertension; Fig. ). All 16 patients (100%) who received autogene cevumeran had grade 1-2 AEs (Extended Data Fig. ). We administered atezolizumab and autogene cevumeran at median times within 1 and 3 days of respective 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. ). Only 1 patient out of 19 (5%) had insufficient neoantigens that led to non-manufacture of the vaccine (Fig. ). Three out of 16 patients (19%) did not receive all 9 vaccine doses (Fig. ),...
Safety, feasibility and immunogenicity
Next, to measure the T cell responses induced by autogene cevumeran, we utilized a previously described ex vivo IFNγ ELISpot assay that detects high-magnitude T cell responses to vaccines without distinguishing 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 cevumeran responders (Fig. ). By testing each specific target included in the neoantigen vaccines, we detected that 25 out of the 230 neoantigens (11%) administered across all patients who were evaluable at the single-target level induced a T cell response of sufficient high magnitude to be detectable by ex vivo IFNγ ELISpot (Fig. and Extended Data Fig. ). Half of all the patients who received the vaccine mounted neoantigen-specific T cell...
T cell clonotypes and phenotypes
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 granzyme B) and cytokines (IFNγ) and resembled effector T cells induced by protective viral vaccines (Fig. and Extended Data Fig. ). Consistently, peripheral blood samples collected after vaccination contained 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. and Extended Data Fig. ) and MHCI-restricted minimal epitopes (Fig. and Extended Data Fig. ). Notably, autogene-cevumeran-expanded T cells maintained functionality despite post-vaccination mFOLFIRINOX treatment...
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Evidence quotes (8)
After surgery, we included patients with pathologically confirmed PDAC with R0/R1 margins. Additional eligibility criteria and ethical study conduct information are in the protocol (Supplementary Data ). We aimed to accrue 20 evaluable patients.
Patients underwent open pancreaticoduodenectomy or either open or laparoscopic distal pancreatectomy and splenectomy at MSK. We then transported tumour blocks with the most (minimum ≥10%) histological tumour content with matched blood to BioNTech.
PDAC is the third leading cause of cancer death in the United States and the seventh worldwide. With an increasing incidence, and a survival rate of 12% that has remained largely stagnant for nearly 60 years, PDAC is projected to cause even greater global cancer deaths by 2025 (refs., ). Surgery is the only curative treatment for PDAC. Yet, despite surgery, nearly 90% of patients have disease recurrence at a median of 7-9 months,, and the 5-year overall survival (OS) is only 8-10%,. 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 months, and their 5-year OS is <30%. Radiation, biologics and targeted therapies are also ineffective.
To test this hypothesis, we conducted an investigator-initiated, phase I clinical trial of sequential adjuvant atezolizumab (Genentech), autogene cevumeran, (an individualized mRNA neoantigen vaccine containing up to 20 major histocompatibility complex class I (MHCI) and MHC class II (MHCII) restricted neoantigens in lipoplex nanoparticles intravenously delivered; Individualized NeoAntigen-Specific Therapy (iNeST), BioNTech and Genentech) and mFOLFIRINOX in patients with surgically resectable PDAC (Fig. ) to: (1) amplify neoantigen-specific T cells inhibited by PD-1 signalling; and (2) prime naive T cells to vaccine neoantigens. 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)...
From December 2019 to August 2021, we enrolled 34 patients, of which 28 patients (Fig. ) 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. ). 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. ). All patients were treated and followed at the Memorial Sloan Kettering 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. ). One out of 16 (6%) patients treated with autogene cevumeran in the safety-evaluable cohort had grade 3 AEs (fever and hypertension; Fig. ). All 16 patients (100%) who received autogene cevumeran had grade 1-2 AEs (Extended Data Fig. ). We administered atezolizumab and autogene cevumeran at median times within 1 and 3 days of respective 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. ). Only 1 patient out of 19 (5%) had insufficient neoantigens that led to non-manufacture of the vaccine (Fig. ). Three out of 16 patients (19%) did not receive all 9 vaccine doses (Fig. ), 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 cevumeran, we utilized a previously described ex vivo IFNγ ELISpot assay that detects high-magnitude T cell responses to vaccines without distinguishing 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 cevumeran responders (Fig. ). By testing each specific target included in the neoantigen vaccines, we detected that 25 out of the 230 neoantigens (11%) administered across all patients who were evaluable at the single-target level induced a T cell response of sufficient high magnitude to be detectable by ex vivo IFNγ ELISpot (Fig. and Extended Data Fig. ). Half of all the patients who received the vaccine mounted neoantigen-specific T cell responses against at least one vaccine neoantigen (median = 2, range = 1-8; Extended Data Fig. ). Furthermore, half of these responses were polytopic, targeting more than one vaccine neoantigen (Fig. ). No T cell responses against vaccine neoantigens were detecta...
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 granzyme B) and cytokines (IFNγ) and resembled effector T cells induced by protective viral vaccines (Fig. and Extended Data Fig. ). Consistently, peripheral blood samples collected after vaccination contained 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. and Extended Data Fig. ) and MHCI-restricted minimal epitopes (Fig. and Extended Data Fig. ). Notably, autogene-cevumeran-expanded T cells maintained functionality despite post-vaccination mFOLFIRINOX treatment, with persistent IFNγ production (Fig. ), uniform re-expansion with a vaccine booster in all responders (Fig. ) and sustained persistence as high as 2.5% of all blood T cells up to 2 years after surgery (Fig. and Supplementary Table ). Furthermore, vaccine boosters re-expanded iden...
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