Combining personalized neoantigen vaccination with chemotherapy and anti-PD-1 to treat NSCLC

In this issue of Cancer Cell, Awad et al. report a phase 1b clinical trial combining a personalized vaccine NEO-PV-01 with chemotherapy and anti-PD-1 pembrolizumab in first-line metastatic non-squamous NSCLC. They demonstrate that this treatment regimen was well tolerated and induced neoantigen-specific CD4+ T cell responses with effector phenotype. In this issue of Cancer Cell, Awad et al. report a phase 1b clinical trial combining a personalized vaccine NEO-PV-01 with chemotherapy and anti-PD-1 pembrolizumab in first-line metastatic non-squamous NSCLC. They demonstrate that this treatment regimen was well tolerated and induced neoantigen-specific CD4+ T cell responses with effector phenotype. Mutations in tumor cells can generate neoantigens that can be presented on the cell surface by major histocompatibility complex (MHC) molecules and subsequently recognized by T cells. Neoantigens are very immunogenic, as they are present only in tumors, but not in normal tissues, and hence circumvent the central thymic tolerance. However, most neoantigens are unique and different from patient to patient, so neoantigen vaccines need to be specifically produced for each patient as personalized vaccines, limiting their clinical use. Recent progress in sequencing and bioinformatics technologies allows rapid identification of candidate neoantigens in individual patients using ad hoc algorithms. Nevertheless, the key challenges are to select appropriate candidates able to trigger tumor-killing T cell responses and to generate the vaccine swiftly with an efficient platform that is easy to manufacture. Two groups overcame these challenges and pioneered an initial set of clinical trials on melanoma patients, demonstrating that personalized neoantigen vaccines are clinically feasible and safe (Ott et al., 2017Ott P.A. Hu Z. Keskin D.B. Shukla S.A. Sun J. Bozym D.J. Zhang W. Luoma A. Giobbie-Hurder A. Peter L. et al.An immunogenic personal neoantigen vaccine for patients with melanoma.Nature. 2017; 547: 217-221https://doi.org/10.1038/nature22991Crossref PubMed Scopus (1703) Google Scholar; Sahin et al., 2017Sahin U. Derhovanessian E. Miller M. Kloke B.P. Simon P. Lower M. Bukur V. Tadmor A.D. Luxemburger U. Schrors B. et al.Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer.Nature. 2017; 547: 222-226https://doi.org/10.1038/nature23003Crossref PubMed Scopus (0) Google Scholar), and have the potential to synergize with immune checkpoint inhibitors (ICIs) such as pembrolizumab (Ott et al., 2017Ott P.A. Hu Z. Keskin D.B. Shukla S.A. Sun J. Bozym D.J. Zhang W. Luoma A. Giobbie-Hurder A. Peter L. et al.An immunogenic personal neoantigen vaccine for patients with melanoma.Nature. 2017; 547: 217-221https://doi.org/10.1038/nature22991Crossref PubMed Scopus (1703) Google Scholar, Ott et al., 2020Ott P.A. Hu-Lieskovan S. Chmielowski B. Govindan R. Naing A. Bhardwaj N. Margolin K. Awad M.M. Hellmann M.D. Lin J.J. et al.A phase Ib trial of personalized neoantigen therapy plus anti-PD-1 in patients with advanced melanoma, non-small cell lung cancer, or Bladder cancer.Cell. 2020; 183: 347-362.e24https://doi.org/10.1016/j.cell.2020.08.053Abstract Full Text Full Text PDF PubMed Scopus (257) Google Scholar). However, the impact of systemic chemotherapy on neoantigen vaccine-induced anti-tumor immunity is unclear. Given that the combination of pembrolizumab and chemotherapy is emerging as a new standard of care for different cancers, such as non-small-cell lung cancer (NSCLC), incorporating neoantigen vaccine in a triple combination therapy may add clinical benefit to patients. Awad et al. report data from a phase 1b clinical trial combining the personalized vaccine NEO-PV-01 with chemotherapy and pembrolizumab in first-line metastatic non-squamous NSCLC (Awad et al., 2022Awad M.M. Govindan R. Balogh K.N. Spigel D.R. Garon E.B. Bushway M.E. Poran A. Sheen J.H. Kohler V. Esaulova E. et al.Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancer.Cancer Cell. 2022; 40https://doi.org/10.1016/j.ccell.2022.08.003Abstract Full Text Full Text PDF PubMed Scopus (21) Google Scholar). NEO-PV-01 is a personalized vaccine comprising up to 20 unique neoantigens per patient, in the form of synthetic long peptides formulated with the TLR3 agonist poly-ICLC as an immune adjuvant. The trial was designed to allow patients to receive standard-of-care treatment, i.e., four cycles of chemotherapy combined with pembrolizumab, during the vaccine production (Figure 1). This single-arm study enrolled 38 patients with no prior systemic treatment for metastatic disease and no prior immunotherapy. Enrollment was not restricted based on tumor PD-L1 status. Patients received at least one dose of pembrolizumab and were defined as the intention-to-treat (ITT) set. Seventeen patients (45%) in the ITT set were not vaccinated due to early study termination for various reasons, mostly the inability to manufacture the vaccine because of low tumor content in the biopsy and/or insufficient number of candidate neoantigens. Only 16 patients completed the vaccination with minor related adverse events reported, showing that NEO-PV-01 in combination with chemotherapy and pembrolizumab was safe and well-tolerated. Molecular and immune analyses of both the tumor microenvironment (TME) and peripheral blood revealed several factors that were correlated with clinical response. T cell infiltration and MHC II expression in the TME at the pre-treatment time point correlated positively with clinical response, in line with previous findings (Cabrita et al., 2020Cabrita R. Lauss M. Sanna A. Donia M. Skaarup Larsen M. Mitra S. Johansson I. Phung B. Harbst K. Vallon-Christersson J. et al.Author correction: tertiary lymphoid structures improve immunotherapy and survival in melanoma.Nature. 2020; 580: E1https://doi.org/10.1038/s41586-020-2155-6Crossref PubMed Scopus (15) Google Scholar; Ganesan et al., 2017Ganesan A.P. Clarke J. Wood O. Garrido-Martin E.M. Chee S.J. Mellows T. Samaniego-Castruita D. Singh D. Seumois G. Alzetani A. et al.Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer.Nat. Immunol. 2017; 18: 940-950https://doi.org/10.1038/ni.3775Crossref PubMed Scopus (328) Google Scholar; Ulloa-Montoya et al., 2013Ulloa-Montoya F. Louahed J. Dizier B. Gruselle O. Spiessens B. Lehmann F.F. Suciu S. Kruit W.H. Eggermont A.M. Vansteenkiste J. Brichard V.G. Predictive gene signature in MAGE-A3 antigen-specific cancer immunotherapy.J. Clin. Oncol. 2013; 31: 2388-2395https://doi.org/10.1200/JCO.2012.44.3762Crossref PubMed Scopus (283) Google Scholar). Also, TCR diversity in the pre-treatment TME had a positive correlation with progression-free survival (PFS), with increased or stable diversity over the course of the study in patients with better PFS. The immune responses elicited by NEO-PV-01 vaccination were assessed in 13 patients with available samples at the pre-vaccine time point compared to the post-vaccine time point (8 weeks after the first vaccine dose). Although immune reactivity to the vaccine epitopes was higher at the post-vaccine time point, only 55% of vaccine peptides elicited a T cell response. Among these responses, 49% were detectable ex vivo in an overnight assay; the rest were detected after a 5-day stimulation with peptides. Hence, only 27% of the candidate epitopes generated a strong immune response. However, all patients responded against at least one epitope with a strong response measurable ex vivo. As expected, responses were usually stronger against the neoepitope as compared to the corresponding wild-type peptide. CD4+ and CD8+ T cell responses were observed against 39% and 31% of the vaccine peptides, respectively. Long-term persistence of the vaccine-induced immune responses was observed after 40 weeks for 85% of the 34 epitopes tested. In 12 patients, the cytotoxic potential of the T cell responses was evaluated by measuring IFNγ and CD107a co-expression on CD4+ and CD8+ T cells recognizing 92 peptides. Co-expression was observed for 61% of the peptides tested, with 11 out of 12 patients showing at least one such response. Surprisingly, these responses were mostly CD4 only responses (93%), while 7% involved both CD4+ and CD8+ T cells, and none involved solely CD8+ T cells. Importantly, epitope spread (Corbiere et al., 2011Corbiere V. Chapiro J. Stroobant V. Ma W. Lurquin C. Lethe B. van Baren N. Van den Eynde B.J. Boon T. Coulie P.G. Antigen spreading contributes to MAGE vaccination-induced regression of melanoma metastases.Cancer Res. 2011; 71: 1253-1262https://doi.org/10.1158/0008-5472.CAN-10-2693Crossref PubMed Scopus (148) Google Scholar; Hu et al., 2021Hu Z. Leet D.E. Allesoe R.L. Oliveira G. Li S. Luoma A.M. Liu J. Forman J. Huang T. Iorgulescu J.B. et al.Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma.Nat Med. 2021; 27: 515-525https://doi.org/10.1038/s41591-020-01206-4Crossref PubMed Scopus (175) Google Scholar) to non-vaccinating epitopes was also investigated and validated. Nine out of 13 (69%) patients had T cell responses against highly ranked neoepitopes that were not included in the vaccine, only at the post-vaccine time point. Interestingly, epitope spread responses were observed toward common driver mutations KRAS G12C and G12V across multiple patients, with 3 out of 4 patients who had epitope spread to a KRAS mutation achieving PFS of at least 9 months after initiation of therapy. A fraction (42%) of the responses to spread epitopes were potentially cytotoxic (CD107a+ IFNγ+), and all of them were CD4 responses. Single-cell sequencing of neoantigen-specific CD4+ T cells suggested an effector cytotoxic phenotype, in line with a potential role of vaccine-induced CD4+ T cells in mediating tumor-cell killing. Nevertheless, a direct proof of the T cell cytotoxic activity on tumor cells is required to consolidate this. Although this study demonstrated the safety and feasibility of NEO-PV-01 in combination with pembrolizumab and chemotherapy as first-line treatment in NSCLC, clinical validation of vaccine efficacy remains to be determined in a randomized trial involving a control arm. Even though clinical responses were observed, most of them started before vaccination and likely resulted from the chemotherapy combined with pembrolizumab. While the combination of NEO-PV-01 with anti-PD-1 was previously shown to be immunogenic (Ott et al., 2020Ott P.A. Hu-Lieskovan S. Chmielowski B. Govindan R. Naing A. Bhardwaj N. Margolin K. Awad M.M. Hellmann M.D. Lin J.J. et al.A phase Ib trial of personalized neoantigen therapy plus anti-PD-1 in patients with advanced melanoma, non-small cell lung cancer, or Bladder cancer.Cell. 2020; 183: 347-362.e24https://doi.org/10.1016/j.cell.2020.08.053Abstract Full Text Full Text PDF PubMed Scopus (257) Google Scholar), the current study indicates that addition of chemotherapy does not hamper immunogenicity of NEO-PV-01. This promising approach faces several challenges. One is the inability to manufacture the vaccine in nearly half of the enrolled patients, because of low amounts of tumor cells in the biopsy or insufficient high-quality neoantigens predicted. Also, some predicted neoantigens were too hydrophobic to be synthesized as long peptides. Another challenge is the difficulty of predicting the processing of the candidate epitopes, which may not be processed and presented at the cell surface. This may contribute to the high percentage (45%) of candidate epitopes that failed to generate a T cell response. Of note, this limitation does not apply to antigens targeted by epitope spreading, which are naturally processed and presented in vivo. Lastly, the poor induction of CD8+ T cells against neoepitopes is likely limiting the anti-tumor efficacy of vaccine-induced immune responses. Even though neoantigen-prediction algorithms largely focused on MHC I epitopes, most vaccine-induced T cell responses are skewed toward CD4 responses. This was also observed in previous studies (Ott et al., 2017Ott P.A. Hu Z. Keskin D.B. Shukla S.A. Sun J. Bozym D.J. Zhang W. Luoma A. Giobbie-Hurder A. Peter L. et al.An immunogenic personal neoantigen vaccine for patients with melanoma.Nature. 2017; 547: 217-221https://doi.org/10.1038/nature22991Crossref PubMed Scopus (1703) Google Scholar, Ott et al., 2020Ott P.A. Hu-Lieskovan S. Chmielowski B. Govindan R. Naing A. Bhardwaj N. Margolin K. Awad M.M. Hellmann M.D. Lin J.J. et al.A phase Ib trial of personalized neoantigen therapy plus anti-PD-1 in patients with advanced melanoma, non-small cell lung cancer, or Bladder cancer.Cell. 2020; 183: 347-362.e24https://doi.org/10.1016/j.cell.2020.08.053Abstract Full Text Full Text PDF PubMed Scopus (257) Google Scholar; Sahin et al., 2017Sahin U. Derhovanessian E. Miller M. Kloke B.P. Simon P. Lower M. Bukur V. Tadmor A.D. Luxemburger U. Schrors B. et al.Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer.Nature. 2017; 547: 222-226https://doi.org/10.1038/nature23003Crossref PubMed Scopus (0) Google Scholar). The reason for this is unclear but may be attributed to the vaccine platforms used in these studies: synthetic long peptides and mRNA. These vaccine platforms may not be able to induce robust CD8+ T cell responses as compared to viral vector vaccines (McAuliffe et al., 2021McAuliffe J. Chan H.F. Noblecourt L. Ramirez-Valdez R.A. Pereira-Almeida V. Zhou Y. Pollock E. Cappuccini F. Redchenko I. Hill A.V. et al.Heterologous prime-boost vaccination targeting MAGE-type antigens promotes tumor T-cell infiltration and improves checkpoint blockade therapy.J Immunother Cancer. 2021; 9e003218https://doi.org/10.1136/jitc-2021-003218Crossref PubMed Scopus (7) Google Scholar), which take longer to manufacture. Different vaccine platforms have their pros and cons, and head-to-head comparisons will yield useful information to further advance cancer vaccine development. In summary, the combination of personalized neoantigen vaccine NEO-PV-01 with pembrolizumab and chemotherapy is safe, practical, and immunogenic, but the anti-tumor efficacy of the vaccine remains to be determined. C.S.K.L. and B.J.V.d.E. are inventors on a patent that covers viral vectors and methods for the prevention and treatment of cancer. B.J.V.d.E. is member of the Scientific Advisory Board of Vaccitech. Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancerAwad et al.Cancer CellAugust 25, 2022In BriefIn a Phase Ib clinical study, Awad et al. demonstrate feasibility, safety, and immunogenicity of NEO-PV-01 plus chemotherapy and PD-1 inhibition in advanced NSCLC as a first-line treatment. Neoantigen-specific CD4+ T cells have an activated effector phenotype. CD4+ T cells infiltrate tumors post-vaccination and induce epitope spread to other neoantigens such as mutant KRAS. Full-Text PDF Open Archive