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CD4 T cell–activating neoantigens enhance personalized cancer vaccine efficacy
Amanda L. Huff, Gabriella Longway, Jacob T. Mitchell, Lalitya Andaloori, Emily Davis-Marcisak, Fangluo Chen, Melissa R. Lyman, Rulin Wang, Jocelyn Mathew, Benjamin Barrett, Sabahat Rahman, James Leatherman, Mark Yarchoan, Nilofer S. Azad, Srinivasan Yegnasubramanian, Luciane T. Kagohara, Elana J. Fertig, Elizabeth M. Jaffee, Todd D. Armstrong, Neeha Zaidi
Amanda L. Huff, Gabriella Longway, Jacob T. Mitchell, Lalitya Andaloori, Emily Davis-Marcisak, Fangluo Chen, Melissa R. Lyman, Rulin Wang, Jocelyn Mathew, Benjamin Barrett, Sabahat Rahman, James Leatherman, Mark Yarchoan, Nilofer S. Azad, Srinivasan Yegnasubramanian, Luciane T. Kagohara, Elana J. Fertig, Elizabeth M. Jaffee, Todd D. Armstrong, Neeha Zaidi
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Research Article Immunology Oncology

CD4 T cell–activating neoantigens enhance personalized cancer vaccine efficacy

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Abstract

Personalized cancer vaccines aim to activate and expand cytotoxic antitumor CD8+ T cells to recognize and kill tumor cells. However, the role of CD4+ T cell activation in the clinical benefit of these vaccines is not well defined. We previously established a personalized neoantigen vaccine (PancVAX) for the pancreatic cancer cell line Panc02, which activates tumor-specific CD8+ T cells but required combinatorial checkpoint modulators to achieve therapeutic efficacy. To determine the effects of neoantigen-specific CD4+ T cell activation, we generated a vaccine (PancVAX2) targeting both major histocompatibility complex class I– (MHCI-) and MHCII-specific neoantigens. Tumor-bearing mice vaccinated with PancVAX2 had significantly improved control of tumor growth and long-term survival benefit without concurrent administration of checkpoint inhibitors. PancVAX2 significantly enhanced priming and recruitment of neoantigen-specific CD8+ T cells into the tumor with lower PD-1 expression after reactivation compared with the CD8+ vaccine alone. Vaccine-induced neoantigen-specific Th1 CD4+ T cells in the tumor were associated with decreased Tregs. Consistent with this, PancVAX2 was associated with more proimmune myeloid-derived suppressor cells and M1-like macrophages in the tumor, demonstrating a less immunosuppressive tumor microenvironment. This study demonstrates the biological importance of prioritizing and including CD4+ T cell–specific neoantigens for personalized cancer vaccine modalities.

Authors

Amanda L. Huff, Gabriella Longway, Jacob T. Mitchell, Lalitya Andaloori, Emily Davis-Marcisak, Fangluo Chen, Melissa R. Lyman, Rulin Wang, Jocelyn Mathew, Benjamin Barrett, Sabahat Rahman, James Leatherman, Mark Yarchoan, Nilofer S. Azad, Srinivasan Yegnasubramanian, Luciane T. Kagohara, Elana J. Fertig, Elizabeth M. Jaffee, Todd D. Armstrong, Neeha Zaidi

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Figure 1

PancVAX plus ICIs elicit antitumoral CD8+ T cell immunity with minimal effect on CD4+ T cells.

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PancVAX plus ICIs elicit antitumoral CD8+ T cell immunity with minimal e...
C57BL/6 mice were implanted with 1 × 106 Panc02s s.c. and vaccinated with PancVAX, s.c. tail base on days 12 and 19. At day 12, mice received 100 µg anti–PD-1, i.p., or isotype twice weekly with 2 doses of 100 µg anti–CTLA-4 or isotype, i.p., on days 15 and 19. (A) Tumor volumes were measured in mice treated with isotype (gray), anti–CTLA-4, and–PD-1 (blue), PancVAX with isotype (yellow), and PancVAX with anti–CTLA-4 and PD-1 (magenta). Shaded regions represent data as mean ± SEM. P values derived from 2-way ANOVA with Tukey’s multiple-comparison test (****P ≤ 0.0001). (B) Survival analysis. P values derived from Log-rank (Mantel-Cox) (***P ≤ 0.001, ****P ≤ 0.0001). (C) Uniform manifold approximation plot (UMAP) of 6,423 T cells from Panc02 tumors (day 35). Cells annotated as cycling T cells (pink), cytotoxic CD8+ T cells (teal), effector CD4+ T cells (gold), exhausted CD8+ T cells (orange), naive CD8+ T cells (blue), and regulatory T cells (olive). UMAP of distribution of T cell populations across groups: Isotype control (gray), anti–CTLA-4, and anti–PD-1 (blue), PancVAX with isotype (yellow), and PancVAX with anti–CTLA-4 and PD-1 (magenta). (D) Stacked bar plot of the proportions of T cell phenotype across groups. (E) Volcano plots of MAST tests for differential expression between Isotype control- and PancVAX-treated, PancVAX + Isotype–treated, and PancVAX + anti–PD-1 + anti–CTLA-4–treated CD8+ T cells in total (top), exhausted CD8+ T cells (middle), and CD4+ T cells (bottom). Genes with significant FDR-adjusted P values (adjusted P < 0.05) and average log2-fold changes (|log2FC| > 0.5) are colored red.

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