Aug 2026· The FEBS Journal· 0 citations· 124 references
Medicine
TL;DR
Recent experimental platforms have been developed to validate neoantigen immunogenicity, which can be complemented by single-cell RNA/T-cell receptor sequencing to identify tumor-reactive T cell clones.
Abstract
Immune checkpoint inhibitors (ICIs), which restore antitumor immunity mediated by T cells, have caused a paradigm shift in cancer therapy. However, only a subset of patients achieve durable clinical responses, highlighting the need to better understand the mechanisms that determine antitumor immunity. Cancer-specific neoantigens are considered key determinants of effective immune responses because they are recognized as non-self by T cells and can induce strong immune responses. Accordingly, neoantigens are considered promising targets for cancer vaccines and adoptive cell therapies. Neoantigens have conventionally been considered to arise from somatic mutations and have been identified using whole-exome sequencing (WES). However, the number of neoantigens identified with WES remains limited. In contrast, advances in technology have revealed that peptides derived from various sources, including noncoding regions, are immunogenic and function as neoantigens. In particular, human leukocyte antigen (HLA) ligandome analyses, which enabled the direct identification of peptides presented on HLA molecules in combination with various sequencing technologies, have extended the landscape of neoantigen sources. However, in many cases, the immunogenicity of the identified neoantigen candidates has not been experimentally evaluated. Recently, several experimental platforms have been developed to validate neoantigen immunogenicity, which can be complemented by single-cell RNA/T-cell receptor sequencing to identify tumor-reactive T cell clones. In this review, we summarize current neoantigen identification strategies and discuss the challenges and future perspectives in neoantigen research.
This review outlines the molecular mechanisms driving neoantigen generation in CRC, including frameshift mutations, single-nucleotide variants, alternative RNA splicing, and circular RNA-derived epitopes, and evaluates neoantigen-directed therapeutic platforms, encompassing personalized neoantigen vaccines and adoptive T-cell therapies that are engineered to recognize neoantigen-derived epitopes.
Na Wang, Yi-Meng Xia, Ping Wang et al.· Medical Oncology· 0 citations
T cells mediate anti-cancer immune responses through recognition of neoantigens - cancer-specific, mutation-derived peptides presented by MHC proteins. “Public” neoantigens are a subset of neoantigens derived from recurrently mutated driver genes and presented by common HLA alleles, making them ideal immunotherapy targets. NRAS is the second most frequently mutated RAS isoform, and its common hotspot mutations (Q61R, Q61K, and Q61L) give rise to a family of HLA-A*01:01 (A1)-restricted public neoantigens.
This study aims to elucidate how the NRAS Q61 neoantigens are structurally and biophysically distinct from their wild-type (WT) counterpart and to resolve the mechanisms that enable a panel of patient-derived TCRs to achieve neoantigen specificity.
Differential scanning fluorimetry shows that each neoantigen and the WT peptide bind A1 with comparable affinity. X-ray crystal structures of the neoantigen/A1 and WT/A1 complexes reveal that the p7Q side chain of the WT peptide is “tethered” to the α2 helix of A1 via a network of hydrogen bonds. This network is disrupted with all neoantigens, increasing the solvent accessibility of the mutated p7 side chains and facilitating potential TCR interactions. In surface plasmon resonance (SPR) binding experiments, one TCR (TCR11L) binds all three neoantigens (Q61R, Q61K, Q61L) and the WT peptide with high affinity. Crystal structures reveal that TCR11L primarily contacts the penultimate p9E of the peptides, bypassing the p7 mutation site. However, T cell-based functional assays show that TCR11L responds only to the Q61K and Q61L neoantigens. Intriguingly, SPR kinetic analyses reveal significantly slower dissociation rates for TCR11L complexed with Q61K and Q61L compared to Q61R and WT, suggesting that the functional specificity of TCR11L is kinetically driven.
Collectively, these biophysical, structural, and functional studies reveal how TCR promiscuity can be exploited to enhance scalability in neoantigen-targeting therapies.
NIH R01CA286507
Vaccines and Immunotherapy (VAC)
Gihan Perera, Iñaki Etxeberria, Christopher A. Klebanoff et al.· Journal of Immunology· 0 citations
ICIs have revolutionized cancer treatment; however, the achievement of sustained clinical benefits is confined to a subset of patients due to inherent and acquired resistance mechanisms. Accumulating evidence suggests that tumor immune evasion is often sustained through intracellular, metabolic, epigenetic, and myeloid-intrinsic pathways, which remain largely inaccessible to antibody-based therapies. These challenges underscore the necessity for supplementary immunotherapeutic approaches that extend beyond cell-surface checkpoint inhibition. Small-molecule immunotherapies present unique pharmacological advantages, such as enhanced tumor infiltration and the ability to target intracellular compartments. This capability facilitates the direct modulation of enzyme-dependent pathways and signaling networks that govern immune suppression within the TME. Recent advancements have unveiled a variety of small-molecule strategies aimed at targeting metabolic immune checkpoints, epigenetic regulators, innate immune sensing pathways, myeloid signaling, and immune checkpoint proteins through non-antibody modalities. Collectively, these strategies have the potential to reprogram the immunotherapy-resistant TME, restore the function of effector immune cells, and enhance responsiveness to ICIs. Clinical successes and failures, underscore the necessity for meticulous consideration of pathway redundancy, dosing, delivery, and biomarker-driven patient selection in the effective translation of small-molecule immunotherapy. Rather than serving as replacements for antibody-based ICIs, small-molecule immunotherapies act as mechanistically complementary agents that facilitate rational combination strategies targeting both surface and intracellular immune resistance mechanisms. In this review, we present a mechanistically integrated overview of small-molecule immunotherapies, examine key translational challenges, and explore future directions for overcoming immune resistance in cancer.
Jin-Man Zhu, Hui-Min Liu, Jing-Ying Hu et al.· International Immunopharmaco...· 0 citations
Personalized neoantigen (neoAg) vaccines have shown clinical promise in solid tumors1–8, yet their efficacy and mechanism of action in hematopoietic malignancies remain poorly defined9–11. Herein, we establish an immunocompetent syngeneic A20 B-cell lymphoma platform to test the efficacy of neoAg vaccines used either as mono- or combinatorial therapies with other immunotherapies12–17. Whereas subcutaneous A20 tumors were refractory to single-agent αPD-1 or αCTLA4 therapy, they were eradicated in a T cell-dependent manner in 90% of syngeneic hosts treated with dual immune checkpoint therapy (dual ICT, i.e., αPD-1 + αCTLA4). By mapping antigen specificity of dual-ICT-elicited T cells, we identified and validated dominant endogenous A20 MHC-I and MHC-II neoantigens and designed therapeutic synthetic long peptide (SLP) vaccines containing these neoepitopes. This vaccine (A20 neoVAX) promoted robust neoAg-specific CD4□ and CD8□ T cell responses in naïve syngeneic BALB/c mice and induced tumor rejection in ∼70% of subcutaneous tumor-bearing mice. In addition, nearly all mice rejected their subcutaneous A20 tumors when A20 neoVAX was combined with αPD-1. To render the results of this study more physiologic, we developed a systemic A20 lymphoma model and found that dual ICT failed to control tumor progression and A20 neoVAX delayed tumor progression and prolonged animal survival but did not induce tumor rejection. In contrast, A20 neoVAX plus dual ICT achieved durable systemic tumor elimination. Mechanistically, the combination of A20 neoVAX plus dual ICT amplified priming of A20 neoAg-specific T cells, prevented T cell dysfunction, sustained the cytotoxic capacity of tumor-specific CD8+ T cells, and induced Th1-skewing of CD4+ T cells in tumor and peripheral compartments. To increase the clinical relevance of these findings and to minimize potential adverse events in tumor-bearing, therapeutically treated individuals, we substituted CD8-targeted cytokine muteins (CD8-IL2 or CD8-IL21) for αCTLA4. These agents represent genetically modified forms of IL-2 or IL-21 that selectively stimulate CD8+ T cells but have significantly reduced capacity to activate chronic inflammation and immunosuppressive functions of other immune cells. Whereas mice bearing systemic A20 lymphoma treated with either nothing, A20 neoVAX, or A20 neoVAX + CD8-IL2 failed to control tumor outgrowth, 66.7% of tumor-bearing mice treated with A20 neoVAX + CD8-IL2 + αPD-1 rejected their tumors. In similar experiments in which CD8-IL21 was substituted for CD8-IL2, tumor clearance was also observed in two-thirds of A20-bearing mice but now rejection occurred in the absence of αPD1. Together, these data define a framework for optimal personalized neoAg vaccination in B-lymphoma and demonstrate that neoAg vaccines can safely synergize with CD8+ T cell-selective immunotherapies to prevent T-cell dysfunction and generate durable systemic anti-tumor immunity.
Yuang Song, E. Aladyeva, Ruan F. Vieira Medrano et al.· bioRxiv· 0 citations
ABSTRACT Cancer immunotherapy has reshaped modern oncology by enabling the immune system to recognize and eliminate malignant cells. However, many solid tumors still respond poorly because of weak T‐cell activation and an immunosuppressive tumor microenvironment. Bacterial superantigens (SAgs) represent a unique class of immunomodulatory proteins capable of overcoming these limitations through direct activation of large T‐cell populations. Unlike conventional antigens, superantigens bypass classical antigen processing by simultaneously binding major histocompatibility complex class II molecules and T‐cell receptor Vβ domains, triggering rapid cytokine release and extensive immune activation. Although this potent mechanism has historically been associated with severe systemic toxicity, recent advances in protein engineering and targeted delivery have renewed interest in their therapeutic potential. This review discusses the structural and immunological basis of superantigen activity and highlights emerging strategies designed to improve tumor specificity and safety, including engineered low‐toxicity variants, antibody‐superantigen fusion proteins, nanoparticle‐based delivery systems, and tumor‐targeted constructs. We further examine how superantigens reshape the tumor microenvironment and synergize with immune checkpoint blockade, adoptive cell therapies, and other T‐cell‐redirecting approaches. Together, these advances position engineered superantigens as promising immune‐amplifying platforms with the potential to complement existing cancer immunotherapies and improve responses in poorly immunogenic tumors.
U. Y. Virk, H. A. Malik, M. Anwer et al.· The FASEB Journal· 0 citations