Personalized neoantigen vaccines for patients with advanced hepatocellular carcinoma

During the last years, immunotherapy based on immune checkpoint inhibitors (ICIs) has gained importance as a new option for patients with hepatocellular carcinoma (HCC). From pioneer studies with monotherapies, based on cytotoxic T-lymphocyte associated protein 4 (CTLA-4) (1) or programmed cell death protein 1 (PD-1) blockade (2), to currently approved combinations [anti PD ligand 1 (antiPD-L1) + anti vascular endothelial growth factor (antiVEGF) or antiPD-L1 + antiCTLA-4] (3,4), response rates have increased from 15% to 25–30%. However, an important proportion of treated patients do not benefit from these therapies, making necessary the development of new strategies. As for other tumors, an important feature determining the response to ICI is the tumor microenvironment (TME). Tumors with a TME containing an enriched lymphocytic infiltrate have higher response rates, while patients with the so-called “cold tumors” usually have poorer responses (5). With this idea, many protocols are aimed at promoting the inflammation of this last group of tumors, to generate a suitable TME for ICI administration.

Vaccination based on the administration of tumor-associated antigens, traditionally used to prime tumor-specific responses, has achieved modest clinical results in cancer patients (6). The immunosuppressive TME and the use of inadequate antigens, with poor immunogenicity and tumor specificity, have been proposed as responsible for these limited results. During the last years, with advances in next generation sequencing methodologies, identification of tumor mutations has allowed the determination of tumor mutational burden (TMB) as a significant parameter in response to immunotherapy (7,8), due to the possibility to generate neoantigens (neoAgs), new immunogenic regions arising as a consequence of these sequence changes. In addition to inducing an antitumor immunity which is rescued by ICI administration, neoAgs are also important in T cell-based adoptive therapies, since an important proportion of T cells used in these therapies are also neoAg-specific (9). These results suggest the pertinence of using neoAgs in vaccine design.

NeoAg vaccines were initially tested in patients with high TMB (e.g., melanoma), demonstrating their safety and immunological efficacy (10-12), and in recent reports, they have been combined with ICI (13,14), where they have shown relevant clinical effects. HCC is a tumor with a moderate TMB (15), where the presence of immunogenic neoAgs has been described (16), and they are associated with patient prognostic (17).

Based on these data, Yarchoan et al. (18) designed a single-arm, open-label, phase 1/2 vaccination clinical trial in patients with advanced HCC, consisting of a personalized neoAg vaccine plus the PD-1 inhibitor pembrolizumab. The trial, with safety and immunogenicity as primary endpoints, and treatment efficacy and feasibility as secondary endpoints, included 36 patients. The vaccine consisted of a DNA plasmid encoding up to 40 personalized neoAgs in combination with other plasmid encoding interleukin 12 (IL-12), as a vaccine adjuvant. As in other neoAg vaccination clinical trials, treatment was safe and well tolerated, with adverse events equivalent to those observed in patients receiving pembrolizumab, plus local reactions at the vaccine injection site.

Regarding clinical response, the objective response rate (ORR) per RECIST 1.1 was 30.6%, with 8.3% of patients with complete response (CR), and 22.2% of partial response (PR). This led to a median progression-free survival of 4.2 months and a median overall survival of 19.9 months. Of note, these clinical results were consistent across sex, etiology and time on first line treatment with other therapies (tyrosine kinase inhibitors). As previously mentioned, ORR with PD-1/PD-L1 inhibitors is in the range of 12–18%, which in the case of pembrolizumab is 16.9%. Although factors such as differences in patient demographics and methodologies may vary between those studies, comparison of these historical results with those obtained in the current vaccine plus pembrolizumab trial suggests a significantly higher ORR value.

Identification of biomarkers of the observed clinical responses showed a lack of association with TMB and with the lymphocytic infiltration, while a positive correlation was observed between the number of neoAgs included in the vaccine and the response to treatment. Analysis of on-treatment responses, both in the tumor and in peripheral blood, showed an increase in biomarkers of T cell activation and infiltration in patients with clinical response. Moreover, neoAg-specific immune responses, both in the number of neoAgs recognized and in the magnitude of the response, were enhanced in most patients after vaccination, with a trend toward a greater magnitude in patients with CR and PR. Increments in T cell immunity were associated with a significant T cell clonal expansion and the presence of new T cell clones after vaccination, which in many cases had features of activated, proliferative and cytolytic cells. Finally, analysis of a patient with a nondurable PR demonstrated the loss of neoAgs and tumor editing, indicating the relevance of responses against these antigens in tumor control.

Results reported by Yarchoan et al. (18) suggest the following comments. First, they demonstrate the feasibility of preparing neoAg-based vaccines with a clinical impact in patients with advanced HCC. Although mutations and neoAgs had been identified in HCC, and even immune responses against high affinity neoAgs showed their association with patient prognosis (17), this is the first work demonstrating that immunogenic neoAgs with capacity to provide a clinical benefit can be identified and used. Different neoAg identification algorithms and pipelines have been reported (19), they have been used to calculate the putative neoAg load, and even to demonstrate the presence of neoAg-specific immunity. However, it was important to demonstrate that HCC patients harbored a sufficient number of neoAgs for vaccine preparation. Indeed, the number of neoAgs used has varied from patient to patient, and better clinical responses have been observed in those patients treated with a vaccine encoding a higher number of neoAgs. In this regard, selection of neoAgs by Yarchoan et al. (18) has been carried out by considering parameters such as expression of the gene containing the mutation, its allelic fraction, self-similarity, and finally, human leukocyte antigen (HLA) binding affinity. By using these criteria, up to 40 neoAgs per patient were selected. Although this selection strategy has proven successful, unfortunately, there are no available data comparing clinical performance of different neoAg identification methods for vaccine design.

Another important aspect relates to the lack of association of clinical responses with the pretreatment TME. As opposed to ICI-based therapies, where clinical responses are mostly observed in patients with an inflamed TME (5), responses found in this trial are independent of the TME. Administration of the neoAg vaccine primes new T cell clones detectable in tumor and blood, generating a new pool of antitumor T cells that can be rescued by antiPD-1 antibodies. Therefore, along with those patients with already existing tumor-specific T cells, a new set of patients where vaccination enlarges the T cell repertoire can be now susceptible to the beneficial effect of ICI, broadening the group of responder patients. In agreement with the previous paragraph, the larger the repertoire of neoAgs targeted by the vaccine, the higher the possibility of priming a new immune response with capacity for tumor control.

ORR achieved in this trial is in the range of those observed when using recently approved combinations (3,4), which do not rely on the complex process of neoAg identification and preparation of the personalized vaccine. However, not all patients may be candidates to these ICI-containing combinations, since vascular endothelial growth factor (VEGF)-targeting approaches may not be appropriate for patients with potential bleeding (20) or the higher toxicity observed for PD-1/PD-L1 and CTLA-4 blockade vs. PD-1/PD-L1-based monotherapies. Combination of a neoAg vaccine with a PD-1-targeting ICI would potentially yield similar results with a lower chance of toxic events in these individuals.

Finally, this approach opens the possibility of using personalized neoAg vaccines in new scenarios. Similar to the increment observed when adding the neoAg vaccine to pembrolizumab, inclusion of the vaccine in triplets containing the vaccine and several ICI or other therapies would potentially result in better responses than those observed when using only ICI combinations. In this respect, a recent clinical trial in pancreatic cancer demonstrated a relevant activity of a combination of a neoAg vaccine plus chemotherapy and PD-1 blockade after surgery (13), indicating the suitability of incorporating the vaccines into combined therapies with already demonstrated activity. Moreover, in addition to patients with advanced HCC, vaccines may also show promise in the adjuvant setting. The low tumor burden present after surgery may avoid the immunosuppressive environment posed by the tumor, presumably facilitating the priming of new antitumor immunity and generating a pool of T cells with capacity to control tumor recurrence. Encouraging results have been recently reported in a phase IIb trial in patients with resected melanoma (stage IIIB–IV), where a combination of a personalized neoAg vaccine plus pembrolizumab resulted in a longer recurrence-free survival vs. pembrolizumab (14), indicating the beneficial effect that these approaches may offer in the adjuvant setting. Activity of ICI in the adjuvant setting has been recently demonstrated in HCC (21), and concurrent combination of ICI with neoAg vaccines would potentially yield even better responses.

In summary, the work reported by Yarchoan et al. demonstrates the feasibility and clinical efficacy of neoAg vaccines in patients with advanced HCC, suggesting the possibility of incorporating this approach to already available therapies. Future studies will be necessary to confirm these results and to demonstrate its suitability in other combinations and in new clinical settings for HCC patients.

Acknowledgments

Funding: This work was supported by Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union and FEDER (No. PI23/00190, to P.S.).

Footnote

Provenance and Peer Review: This article was commissioned by the editorial office, AME Clinical Trials Review. The article has undergone external peer review.

Peer Review File: Available at https://actr.amegroups.com/article/view/10.21037/actr-24-76/prf

Conflicts of Interest: Both authors have completed the ICMJE uniform disclosure form (available at https://actr.amegroups.com/article/view/10.21037/actr-24-76/coif). P.S. is currently funded by Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union and FEDER (No. PI23/00190). The other author has no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

References

1. Sangro B, Gomez-Martin C, de la Mata M, et al. A clinical trial of CTLA-4 blockade with tremelimumab in patients with hepatocellular carcinoma and chronic hepatitis C. J Hepatol 2013;59:81-8. [Crossref] [PubMed]
2. El-Khoueiry AB, Sangro B, Yau T, et al. Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, phase 1/2 dose escalation and expansion trial. Lancet 2017;389:2492-502. [Crossref] [PubMed]
3. Finn RS, Qin S, Ikeda M, et al. Atezolizumab plus Bevacizumab in Unresectable Hepatocellular Carcinoma. N Engl J Med 2020;382:1894-905. [Crossref] [PubMed]
4. Abou-Alfa GK, Lau G, Kudo M, et al. Tremelimumab plus Durvalumab in Unresectable Hepatocellular Carcinoma. NEJM Evid 2022;1:EVIDoa2100070.
5. Zhu AX, Abbas AR, de Galarreta MR, et al. Molecular correlates of clinical response and resistance to atezolizumab in combination with bevacizumab in advanced hepatocellular carcinoma. Nat Med 2022;28:1599-611. [Crossref] [PubMed]
6. Saxena M, van der Burg SH, Melief CJM, et al. Therapeutic cancer vaccines. Nat Rev Cancer 2021;21:360-78. [Crossref] [PubMed]
7. Yarchoan M, Hopkins A, Jaffee EM. Tumor Mutational Burden and Response Rate to PD-1 Inhibition. N Engl J Med 2017;377:2500-1. [Crossref] [PubMed]
8. Jardim DL, Goodman A, de Melo Gagliato D, et al. The Challenges of Tumor Mutational Burden as an Immunotherapy Biomarker. Cancer Cell 2021;39:154-73. [Crossref] [PubMed]
9. Aparicio B, Theunissen P, Hervas-Stubbs S, et al. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024;20:2303799. [Crossref] [PubMed]
10. Carreno BM, Magrini V, Becker-Hapak M, et al. Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 2015;348:803-8. [Crossref] [PubMed]
11. Ott PA, Hu Z, Keskin DB, et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 2017;547:217-21. [Crossref] [PubMed]
12. Sahin U, Derhovanessian E, Miller M, et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 2017;547:222-6. [Crossref] [PubMed]
13. Rojas LA, Sethna Z, Soares KC, et al. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 2023;618:144-50. [Crossref] [PubMed]
14. Weber JS, Carlino MS, Khattak A, et al. Individualised neoantigen therapy mRNA-4157 (V940) plus pembrolizumab versus pembrolizumab monotherapy in resected melanoma (KEYNOTE-942): a randomised, phase 2b study. Lancet 2024;403:632-44. [Crossref] [PubMed]
15. Alexandrov LB, Nik-Zainal S, Wedge DC, et al. Signatures of mutational processes in human cancer. Nature 2013;500:415-21. [Crossref] [PubMed]
16. Repáraz D, Ruiz M, Llopiz D, et al. Neoantigens as potential vaccines in hepatocellular carcinoma. J Immunother Cancer 2022;10:e003978. [Crossref] [PubMed]
17. Liu T, Tan J, Wu M, et al. High-affinity neoantigens correlate with better prognosis and trigger potent antihepatocellular carcinoma (HCC) activity by activating CD39(+)CD8(+) T cells. Gut 2021;70:1965-77. [Crossref] [PubMed]
18. Yarchoan M, Gane EJ, Marron TU, et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med 2024;30:1044-53. [Crossref] [PubMed]
19. Xie N, Shen G, Gao W, et al. Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023;8:9. [Crossref] [PubMed]
20. Ha Y, Kim JH, Cheon J, et al. Risk of Variceal Bleeding in Patients With Advanced Hepatocellular Carcinoma Receiving Atezolizumab/Bevacizumab. Clin Gastroenterol Hepatol 2023;21:2421-2423.e2. [Crossref] [PubMed]
21. Qin S, Chen M, Cheng AL, et al. Atezolizumab plus bevacizumab versus active surveillance in patients with resected or ablated high-risk hepatocellular carcinoma (IMbrave050): a randomised, open-label, multicentre, phase 3 trial. Lancet 2023;402:1835-47. [Crossref] [PubMed]