As research into cancer treatment advances, neoantigens are emerging as promising targets for immunotherapy. These unique markers, arising from genetic mutations within tumor cells, present opportunities for highly specific and effective cancer treatments. This guide explores the landscape of neoantigen-based immunotherapies, focusing on their potential application and advancements in mesothelioma and other cancers.
Neoantigens, distinct from normal cellular components, trigger potent T cell responses due to their novelty to the immune system. This characteristic makes them ideal targets for cancer immunotherapies, including vaccines, adoptive cell therapies (ACTs), and antibody-based treatments. Moreover, neoantigens are being investigated as potential predictive biomarkers for the effectiveness of immune checkpoint inhibitors (ICBs).
Neoantigens can be categorized as personalized, unique to each patient’s tumor, or shared, present across multiple patients with the same cancer type. While personalized neoantigens offer tailored treatment approaches, shared neoantigens pave the way for off-the-shelf therapies, reducing the time and resources required for development. The advent of high-throughput sequencing has revolutionized the identification of personalized neoantigens, enabling the immune system to precisely target malignant cells based on their unique immunogenic epitopes, without relying on pre-defined public antigens.
Neoantigen-Based Therapeutic Vaccines: A Primer
Neoantigen vaccines represent a promising strategy to stimulate and enhance anti-tumor T cell responses. Their feasibility, safety profile, and relative ease of manufacturing make them attractive candidates for cancer immunotherapy. Various vaccine formats, including peptide, nucleic acid, and dendritic cell (DC) vaccines, are currently under clinical evaluation for different cancer types, including those with limited treatment options such as mesothelioma.
Peptide Vaccines: Precision Targeting with Proven Safety
Peptide-based neoantigen vaccines have garnered significant attention, particularly in personalized cancer treatment strategies. Their high specificity, cost-effectiveness in production, and established safety records are key advantages. Neoantigen peptides, either long, genetically encoded, or short, chemically synthesized, undergo purification processes to ensure sterility and high purity. These peptides, combined with adjuvants, are then administered via subcutaneous injection to stimulate an immune response.
Clinical trials have demonstrated the potential of peptide neoantigen vaccines in inducing specific cytotoxic T lymphocyte (CTL) responses and preventing disease progression in certain cancers. These vaccines, designed to target specific mutations, have shown minimal adverse reactions, highlighting their safety profile. To address tumor heterogeneity and HLA diversity, researchers are exploring overlapping peptides or long multi-epitope peptides to elicit robust T cell responses. Immunostimulatory adjuvants and multimeric formulations are also being developed to further enhance the immunogenicity of these personalized peptide vaccines. Clinical studies have evaluated personalized neoantigen vaccines based on synthetic peptides across various cancers, showcasing their broad applicability.
Nucleic Acid Vaccines: DNA and RNA Approaches
Nucleic acid vaccines, encompassing RNA and DNA vaccines, share the benefits of peptide vaccines, including low cost and non-HLA specificity. These vaccines can deliver multiple tumor neoantigens in a single administration, triggering both cellular and humoral anti-tumor immune responses.
mRNA Vaccines: Harnessing the Power of Genetic Code
mRNA technology has emerged as a versatile tool in cancer therapy, exemplified by the success of COVID-19 mRNA vaccines. mRNA vaccines offer significant advantages, including safety, high potency, rapid and cost-effective production, and the ability to encode entire antigens. In vitro transcription (IVT) is the primary method for mRNA vaccine production, followed by purification and encapsulation in delivery systems like liposomes to facilitate cellular uptake and neoantigen translation. Personalized mRNA vaccines, targeting tumor-specific neoantigens, elicit potent immune responses due to the absence of central immune tolerance. Clinical trials are underway to assess the efficacy of personalized mRNA vaccines, both as monotherapy and in combination with PD-1 inhibitors, demonstrating promising results in inducing neoantigen-specific T cell responses.
mRNA vaccines may offer advantages over peptide vaccines due to mRNA’s role as a template for protein synthesis, enabling post-translational modifications and presentation of diverse epitopes without HLA restriction. The ability to incorporate numerous neoantigen epitopes into a single mRNA backbone further enhances their potential. Effective delivery of mRNA vaccines requires maintaining mRNA stability and efficient intracellular delivery. Nanoformulations, particularly lipid nanoparticles, play a crucial role in protecting mRNA from degradation and enhancing delivery efficiency. Clinical trials are exploring lipid nanoparticle-mRNA formulations, demonstrating their potential in inducing robust immune responses. The route of administration is also a critical factor, with intravenous administration showing promise for mRNA-lipoplex vaccines in inducing stronger T cell responses.
DNA Vaccines: Stability and Versatility
DNA vaccines offer a multifunctional platform characterized by stability, ease of manufacturing, cost-effectiveness, and simple storage. DNA vaccines can accommodate large sequences without compromising stability, are rapidly produced in bacteria like E. coli, and can be stored without complex cold-chain logistics. Plasmid DNA, encoding predicted neoantigens, is delivered intramuscularly or subcutaneously, often with electroporation, to induce neoantigen expression and immune responses. DNA vaccines stimulate both humoral and cellular immunity, along with innate immune responses triggered by the double-stranded DNA structure. Rational neoantigen selection is crucial for enhancing DNA vaccine immunogenicity and overcoming immune tolerance. Optimized polyepitope neoantigen DNA vaccines have shown therapeutic efficacy in preclinical models, and combination with anti-PD-1 therapy has demonstrated synergistic tumor control. Clinical trials are evaluating neoantigen-based DNA vaccines for various solid tumors, highlighting their potential in cancer immunotherapy.
While mRNA and DNA vaccines are still evolving compared to ICBs and T cell therapies, ongoing advancements in formulation and preparation are paving the way for their broader clinical application in personalized neoantigen-based cancer treatments.
Dendritic Cell Vaccines: Harnessing Nature’s Antigen Presenters
Dendritic cells (DCs), acting as antigen-presenting cells (APCs), are crucial for initiating immune responses. Autologous DCs, isolated from patients, can be loaded with neoantigens ex vivo and reintroduced to stimulate neoantigen-specific immune responses. This approach leverages DCs’ natural ability to present antigens and activate T cells, potentially expanding the breadth and diversity of anti-tumor immunity. Clinical trials are investigating the safety and efficacy of personalized neoantigen DC vaccines in various solid tumors, including mesothelioma and other cancers with limited treatment options.
Neoantigens can be loaded onto DCs using diverse techniques, including mRNA transfection, synthetic peptide pulsing, autologous whole tumor lysate (WTL) pulsing, and fusion with tumor cells. mRNA transfection offers a straightforward method for intracellular neoantigen production in DCs, and can also deliver functional proteins to enhance DC activation. Peptide pulsing provides a targeted approach, requiring accurate neoantigen epitope prediction and synthesis. WTL pulsing offers a broader antigen presentation, while DC-tumor cell fusion enhances co-stimulation capacity. Clinical studies have demonstrated the safety and effectiveness of neoantigen-loaded DC vaccines in inducing anti-tumor immunity and eliciting clinical responses in various malignancies.
Neoantigen-Based Adoptive Cell Therapies (ACTs): Amplifying Immune Power
Neoantigens, with their high immunogenicity, serve as excellent targets for ACT, which utilizes a patient’s own or genetically engineered anti-tumor lymphocytes. Neoantigen-based ACTs, including tumor-infiltrating lymphocytes (TILs) and genetically engineered immune cells with novel T cell receptors (TCRs) or chimeric antigen receptors (CARs), are demonstrating success in treating various malignancies.
Adoptive Transfer of TILs: Harnessing the Body’s Natural Defenders
CD8+ T lymphocytes, capable of recognizing and eliminating cancer cells, are central to TIL therapy. Autologous TILs, isolated from a patient’s tumor, are expanded in vitro and reinfused to enhance their anti-cancer activity. TILs enriched for neoantigen specificity are particularly effective in achieving tumor regression. Neoantigen-specific TCRs often exhibit higher avidities compared to tumor antigen-specific TCRs, enabling potent responses even at low antigen levels. Adoptive transfer of TILs enriched in neoantigen-targeted T cells holds promise even for tumors with low mutational burden, like some mesotheliomas.
Neoantigen-reactive TILs have shown remarkable tumor regression in epithelial cancers, including advanced breast cancer, metastatic cholangiocarcinoma, colorectal cancer, melanoma, and cervical cancers. Studies have highlighted the role of neoantigen-specific CD4+ T cells in controlling metastatic epithelial cancers. Even in gastrointestinal cancers, where shared immunogenic epitopes are rare, prevalent driver mutations like KRAS-G12D can be targeted by CD8+ TILs. TIL therapy has shown efficacy in treating patients with metastatic malignancies refractory to conventional therapies, including chemotherapy, radiotherapy, and anti-PD-1 therapies. The frequency and breadth of TILs are critical determinants of therapeutic efficacy, and ongoing research focuses on optimizing TIL quality and tumor reactivity.
Genetically Engineered Anti-Tumor Immune Cells: Precision Immune Engineering
Genetic modification of immune cells, including T cells, natural killer (NK) cells, and macrophages, enables the generation of TCRs and CARs that specifically target neoantigens. This approach overcomes limitations associated with the proportion of tumor antigen-reactive TILs. Neoantigens, derived from tumor-specific somatic mutations, are primary targets for engineered immune cells, offering promising effects in solid tumor treatment. Neoantigen-targeted TCR-T and CAR-T therapies are actively being investigated in clinical trials, demonstrating intriguing therapeutic potential for cancers like mesothelioma that often lack effective targeted therapies.
TCR-T Cells: Redirecting T Cell Specificity
TCR-transduced T cells can target both surface and intracellular antigens. Researchers have established efficient approaches for neoantigen identification and engineering of neoantigen-targeting cytotoxic TCR-T cells. Identified neoantigens and their corresponding T cells are used to sequence TCRs. Candidate TCR sequences with neoantigen reactivity are then introduced into T cells using gene editing technologies. These engineered cells, expressing neoantigen-specific TCRs, are verified for tumor reactivity before infusion into patients. Engineered high-avidity TCRs enable CD8+ T cells to specifically target neoantigen-containing tumors. Clinical trials are evaluating the safety and efficacy of autologous T cells engineered to express TCRs targeting public neoantigens, such as KRAS mutations, and personalized neoantigen-specific TCRs in various solid tumors. Non-viral precision genome editing techniques are accelerating the production of clinical-grade TCR-T cells, allowing for faster development of personalized T cell therapies.
CAR-T Cells: MHC-Independent Targeting
CAR-T cell therapy offers a significant advantage over TCR-T cells by bypassing the need for HLA expression and neoantigen presentation, mechanisms often exploited by cancer cells for immune evasion. CAR molecules, engineered with an extracellular antigen-binding domain and intracellular signaling domains, enable CAR-T cells to bind cell surface proteins and activate independently of MHC. While early CAR-T cell successes were primarily in B-cell malignancies, neoantigens are inspiring creative solutions for solid tumors. CAR-T cells are being engineered with single-chain variable fragments (scFvs) that recognize neoantigenic peptide-MHC complexes on tumor cells. Clinical trials are ongoing to test CAR-T cells targeting novel neoantigens in hematological and solid tumors, including those relevant to mesothelioma. Neoantigens like EGFRvIII mutation in glioblastoma are being targeted with CAR-T therapy. Strategies to enhance CAR-T cell specificity and efficacy, such as Boolean logic gates and synNotch-regulated CAR activation, are under development to address tumor heterogeneity and improve anti-tumor immunity.
CAR-NK Cells: MHC-Independent Cytotoxicity
NK cells, like CD8+ cytotoxic T cells, can be engineered to express CARs. CAR-NK cells offer MHC-independent cytotoxicity, making them potential immunotherapies for tumors with low mutational burden and deficient neoantigen presentation, which can be relevant for certain subtypes of mesothelioma. Arming NK cells with neoepitope-specific CARs enhances their anti-tumor responses without off-target toxicity. CAR-NK cells also prime DC maturation and neoantigen presentation, and recruit neoantigen-specific CD8+ T cells, expanding the applicability of CAR-based immunotherapy to a broader range of cancers.
Antibody-Based Therapy Against Neoantigens: Precision Targeting with Antibodies
Antibody therapies, exemplified by ICBs, have revolutionized cancer treatment. TCR-mimic (TCRm) antibodies and mutation-associated neoantigen (MANA)-specific antibodies can recognize intracellular neoantigens by targeting peptide-MHC (pMHC) complexes. TCRm antibodies often exhibit higher affinity than TCRs, crucial for minimizing off-tumor effects. These neoantigen-targeted antibodies can be developed in various therapeutic formats, including full-length antibodies, antibody-drug conjugates (ADCs), and bispecific antibodies (BsAbs). TCRm antibody moieties can also drive specific activity in CAR-T therapy, demonstrating remarkable efficacy in certain cancers. Antibody-based strategies offer the potential for off-the-shelf products targeting public neoantigens, benefiting a broader patient population.
Technologies like phage display, yeast display, and genetic platforms are used to identify human TCRm antibodies with high specificity for neoantigens presented on HLA. High-throughput genetic platforms like PresentER aid in assessing the on- and off-targets of TCRm antibodies. Structural analysis and library screening enhance TCRm antibody specificity evaluations. Public neoantigens derived from recurrent driver mutations in oncogenes like EGFR, KRAS, PIK3CA, and CTNNB1 are being targeted with antibody-based therapies. ScFvs targeting these public neoantigens are being developed into therapeutic formats. TCRm antibodies targeting public neoantigens from oncogene mutations offer potential for broad application.
Public neoantigens from tumor suppressor genes (TSGs) are challenging targets, but TCRm antibodies are being developed to address this. The TSG p53, despite being intracellular, is being targeted with TCRm antibodies. Tumors with mutant p53 may overexpress wild-type p53 peptide, which can be presented by MHC molecules, differentiating them from healthy cells. TCR-like antibodies like P1C1TM, specific for wild-type p53 peptide/HLA-A24:02 complex, can target mutant p53 tumors. P1C1TM-ADCs are being developed to deliver cytotoxic payloads specifically to mutant p53-expressing tumors.
BsAbs, such as bispecific T cell engagers (BiTEs), address the issue of low pMHC complex density on the cell surface. BiTEs simultaneously bind neoantigens on tumor cells and CD3 on T cells, enhancing T cell activation. BsAbs targeting mutant p53 pMHC complexes are being developed to overcome the undruggable reputation of p53. Dimeric T cell engaging bsAbs are also being created based on human TCRm antibodies targeting mutant LMP2A peptide-HLA-A*02:01 and mutant RAS peptide-HLA complexes, demonstrating efficacy in activating T cells and killing target cancer cells. Immune-mobilizing monoclonal TCRs against cancer (ImmTACs) are another class of bispecific molecules that guide T cells to kill cancer cells, even with low surface epitope concentrations. TCRm antibody-based strategies are expanding the reach of targeted anti-cancer therapies to neoantigens from both oncogenes and TSGs. Careful screening and negative selection are essential to prevent cross-reactivity of TCRm antibodies.
Combinational Therapies: Synergizing Neoantigen Immunotherapies
The heterogeneity of neoantigen landscapes and evolving cancer immune evasion mechanisms necessitate combination therapies to enhance treatment efficacy. Combining immunotherapies targeting different stages of the cancer-immunity cycle can improve outcomes. Another strategy involves combining immunotherapies with conventional treatments like radiotherapy and chemotherapy to overcome resistance arising from tumor heterogeneity.
Neoantigen-Based Immunotherapies and ICBs: Unleashing T Cell Potential
Immune checkpoint inhibitor (ICB) therapy, while effective in some cancers, often requires the presence of tumor-specific effector T cells. ICBs primarily target specific phases of the anti-cancer immunity pathway. Combining ICBs with neoantigen-based immunotherapies aims to enhance tumor-reactive T cell responses. Clinical trials are exploring combinations of neoantigen vaccines, such as mRNA vaccines, with ICBs for solid tumors, including mesothelioma. Neoantigen vaccines can upregulate immunosuppressant regulators, which ICBs can mitigate, leading to enhanced and durable CD8+ T cell control. The combination of neoantigen vaccines and ICBs holds promise for achieving improved anti-tumor immune responses in mesothelioma and other cancers. ICB therapy can further boost the anti-tumor efficacy of CTLs, including neoantigen-specific CTLs. ICBs can promote the infiltration of neoantigen-reactive lymphocytes into tumors and reinvigorate exhausted neoantigen-specific T cells by overcoming the suppressive tumor microenvironment.
Combinations of Neoantigen Vaccine and ACT: Priming and Amplifying
Combining neoantigen vaccination and ACT has shown success in enhancing clinical efficacy. Vaccination can increase circulating neoantigen-reactive T cells and induce de novo T cell responses. Vaccines can also protect neoantigen-reactive T cells from immune checkpoint signaling, facilitating tumor infiltration and durable tumor reduction. Vaccines can be used to prime neoantigen-reactive TILs or PBMCs before in vitro T cell culture for ACT, potentially inducing memory T cell responses and improving ACT efficacy. Vaccines are also being used to enhance CAR-T cell therapy efficacy in solid tumors. Booster vaccines for CAR-T cells, delivering peptide neoantigens to lymph nodes, can enhance CAR-T cell function in vivo. Amph-ligand vaccines can amplify and promote intratumoral infiltration of CAR-T cells, demonstrating the promise of neoantigen vaccine and CAR-T cell combinatorial therapy.
Neoantigen-Based Immunotherapies and Conventional Therapies: Integrating Treatment Modalities
Conventional therapies like chemotherapy and radiotherapy can be integrated with neoantigen-based immunotherapies to enhance treatment outcomes. Chemotherapy and radiotherapy can increase the release of tumor-specific neoantigens, addressing the challenge of insufficient neoantigen levels for stimulating T cell responses. Radiotherapy can upregulate neoantigenic mutations and enhance MHC-I expression on tumor cells, promoting cell killing by neoantigen-specific CD8+ T cells. Neoantigen vaccines based on radiotherapy-induced immunogenic mutations can elicit CD8+ and CD4+ T cells, improving radiotherapy efficacy. However, radiation-induced subclonal neoantigens may pose challenges, requiring further investigation into combined radiation, DDR inhibitors, and neoantigen-based therapies. Reversion mutations arising during chemotherapy and targeted therapy can encode tumor-specific neoantigens, offering opportunities to combat resistance with CAR-T cell therapies, ICBs, or anti-cancer vaccines. Pretreatment with cyclophosphamide and other drugs can enhance the amount and activity of neoantigen-specific T lymphocytes, improving vaccine efficacy. These studies demonstrate the potential of combining conventional treatments with neoantigen-based immunotherapies to achieve improved tumor control.
Conclusion
Neoantigen-based immunotherapies represent a rapidly evolving field with immense potential to transform cancer treatment, including challenging cancers like mesothelioma. From personalized vaccines to sophisticated adoptive cell therapies and targeted antibodies, these approaches leverage the unique nature of tumor-specific neoantigens to elicit precise and potent immune responses. Ongoing research into combination therapies, integrating neoantigen-based strategies with ICBs, ACTs, and conventional treatments, is paving the way for more effective and durable cancer control. As our understanding of neoantigens and the tumor microenvironment deepens, these innovative immunotherapies hold the promise of significantly improving outcomes for patients facing mesothelioma and other malignancies.
