A Neoantigen-Based Peptide Vaccine for Patients With Advanced Pancreatic Cancer Refractory to Standard Treatment

Abstract

Background: Neoantigens are critical targets to elicit robust antitumor T-cell responses. Personalized cancer vaccines developed based on neoantigens have shown promising results by prolonging cancer patients' overall survival (OS) for several cancer types. However, the safety and efficacy of these vaccine modalities remains unclear in pancreatic cancer patients.

Methods: This retrospective study enrolled 7 advanced pancreatic cancer patients. Up to 20 neoantigen peptides per patient identified by our in-house pipeline iNeo-Suite were selected, manufactured and administered to these patients with low tumor mutation burden (TMB) (less than 10 mutations/Mb). Each patient received multiple doses of vaccine depending on the progression of the disease. Peripheral blood samples of each patient were collected pre- and post-vaccination for the analysis of the immunogenicity of iNeo-Vac-P01 through ELISpot assay and flow cytometry.

Results: No severe vaccine-related adverse effects were witnessed in patients enrolled in this study. The mean OS, OS associated with vaccine treatment and progression free survival (PFS) were reported to be 24.1, 8.3 and 3.1 months, respectively. Higher peripheral IFN-γ titer and CD4+ or CD8+ effector memory T cells count post vaccination were found in patients with relatively long overall survival. Remarkably, for patient P01 who had a 21-month OS associated with vaccine treatment, the abundance of antigen-specific TCR clone drastically increased from 0% to nearly 100%, indicating the potential of iNeo-Vac-P01 in inducing the activation of a specific subset of T cells to kill cancer cells.

Conclusions: Neoantigen identification and selection were successfully applied to advanced pancreatic cancer patients with low TMB. As one of the earliest studies that addressed an issue in treating pancreatic cancer with personalized vaccines, it has been demonstrated that iNeo-Vac-P01, a personalized neoantigen-based peptide vaccine, could improve the currently limited clinical efficacy of pancreatic cancer.

Clinical trial registration: ClinicalTrials.gov, identifier (NCT03645148).Registered August 24, 2018 - Retrospectively registered.

Keywords: immunotherapy; neoantigen; pancreatic cancer; peptide; vaccine.

Conflict of interest statement

FM is an employee for Hangzhou Neoantigen Therapeutics Co., Ltd and Hangzhou Al-Force Therapeutics. SZ, NH, DM, HW, XG, KL, MQ, QH, LL, and SC are employees for Hangzhou Neoantigen Therapeutics Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Copyright © 2021 Chen, Zhang, Han, Jiang, Xu, Ma, Lu, Guo, Qiu, Huang, Wang, Mo, Chen and Yang.

Figures

Figure 1

Clinical treatment process for each patient from surgery or primary visit until the end of follow-up.

Figure 2

The clinical response and prognosis of treated patients. (A) The overall survival curve of each patient. (B) The percentage changes of tumor lesion in size from baseline. The changes in lesions between a positive value of 25% and a negative value of 50% are considered stable disease.

Figure 3

A case report of Patient P01. (A) Treatment timeline of P01. (B) Comparison of lymph node before & after vaccination by imaging. (C, D)Ex vivo IFN-γ ELISpot of PBMCs was performed with peptides at different time points. The dimethyl sulfoxide (DMSO) group was used as the negative control and mixed peptides from CEF (including peptides of cytomegalovirus, Epstein–Barr virus and influenza virus) were used as the positive control. (E) Increased abundance of peripheral T cell clones after vaccination was detected by TCR sequencing.

Figure 4

Immune Response induced by iNeo-Vac-P01. (A) iNeo-Vac-P01 induced specific T cell response. For each patient marked in X-axis, green triangle and red diamond represent the response rates pre- and post-vaccination, defined as the ratios of the numbers of peptides (or peptide pools) with positive ELISpot results before and after vaccination to the total number of peptides (or peptide pools) in vaccine, respectively. The bar chart with secondary Y-axis represented the IFN-γ spots per 105 PBMCs of the peptide with best response for each patient. (B) Change in T cell subsets count at baseline and 22 days post iNeo-Vac-P01 vaccination. Blue and yellow dots represent the cell counts at baseline and 22 days post iNeo-Vac-P01, respectively. Grey dots represent the fold change of corresponding cell count, which can be read at the right Y-axis. Counts of T cell subsets including CD4+ central memory, CD4+ effector memory, CD8+ central memory and CD8+ effector memory T cells were compared in long OS patients (shown in dark grey) and short OS patients (shown in light grey). *: significant, p=0.01 to 0.05; **: very significant, p=0.001 to 0.01; ns: not significant.

Figure 5

The proportion of CTLA4+ T cells in peripheral blood increased after vaccination. The proportions of CD8+ CTLA-4+ T cells and CD4+ CTLA-4+ T cells ratio to total T cells in peripheral blood were determined by flow cytometry. Fold changes of post vaccination compared with baseline were calculated.