Feb 25, 2025

Understanding Neoantigens

The field of immunotherapy has witnessed remarkable advancements over the past decade, with neoantigens emerging as a cornerstone of personalized cancer treatment. Neoantigens, which are tumor-specific antigens arising from somatic mutations, have opened new avenues for developing highly targeted therapies. Their unique ability to elicit robust immune responses without harming healthy tissues has positioned them as a promising tool in the fight against cancer. In this article, we will explore the clinical applications of neoantigens, their role in modern immunotherapy, and the challenges and opportunities they present.

What Are Neoantigens?

Neoantigens are peptides derived from non-synonymous mutations in tumor DNA. These mutations result in the production of proteins that are entirely foreign to the immune system, making them ideal targets for immune recognition. Unlike traditional tumor-associated antigens (TAAs), which are also expressed in normal tissues, neoantigens are exclusive to cancer cells. This specificity minimizes the risk of off-target effects and autoimmune reactions, making neoantigen-based therapies highly attractive.

Mechanism of Action

In terms of the mechanism of action, after tumor cells generate neoantigens, these antigens will be processed by the intracellular antigen-processing machinery and presented on the major histocompatibility complex (MHC) molecules on the cell surface. T cells in the immune system recognize these neoantigens presented on MHC through their T-cell receptors (TCRs) and are thus activated. The activated T cells rapidly proliferate and differentiate into effector T cells, which can precisely recognize and kill tumor cells carrying the corresponding neoantigens, initiating the body's immune attack against tumors.

The identification of neoantigens has been revolutionized by advancements in next-generation sequencing (NGS) technologies, genomic sequencing for cancer treatment, and bioinformatics¹. By analyzing tumor genomes, researchers can pinpoint mutations that give rise to neoantigens and predict their binding affinity to major histocompatibility complex (MHC) molecules. This process, known as neoantigen prediction, is critical for designing personalized cancer immunotherapies.

Additionally, immunopeptidomic analysis using mass spectrometry (MS) has significantly advanced the validation of neoantigens. For instance, the application of MS to identify HLA-bound peptides, in combination with proteogenomics, has facilitated the exploration of novel targets from various antigens naturally processed and presented in cancer, including neoantigens. This approach allows for the identification of tumor-specific antigens that are presented on the surface of cancer cells, which is crucial for developing personalized cancer immunotherapies.

Neoantigen Discovery Workflow. “In typical neoantigen identification workflows, candidate tumor antigens are defined from next-generation sequencing data (left side). Subsequent in silico binding predictions and in vitro immunogenicity tests identify potential tumor neoepitopes, which, however, are not necessarily presented on the tumor cells themselves. If the target epitope is not present, CD8+ T cells cannot identify the transformed cells and the tumor proliferates (middle). In contrast, mass spectrometry-based immunopeptidomics identifies truly presented and actionable epitopes. Immunotherapies targeting these epitopes lead to an immune attack by CD8+ T cells and tumor destruction (right side).” Created with BioRender.com. Retrieved from Becker and Riemer, 2022, with modified labels for clarity.² https://creativecommons.org/licenses/by/4.0/.

Neoantigen Clinical Applications

Neoantigen-Based Cancer Vaccines

One of the most promising applications of neoantigens is the development of personalized cancer vaccines³. These vaccines are designed to stimulate the patient’s immune system to recognize and attack tumor cells expressing the targeted neoantigens.

A landmark study published in Nature⁴ demonstrated the potential of neoantigen peptide vaccines in melanoma patients. Researchers identified neoantigens specific to each patient’s tumor, synthesized corresponding peptides, and administered them as a vaccine. The results were striking: the vaccines induced robust T-cell responses and led to tumor regression in several patients.

Similar success has been observed in other cancer types, including glioblastoma and non-small cell lung cancer (NSCLC). For instance, phase I trials in glioblastoma patients showed that neoantigen peptide vaccines could elicit durable immune responses and improve progression-free survival^{5, 6}. These findings underscore the potential of neoantigen vaccines as a powerful tool in personalized oncology.

Adoptive Cell Therapy with Neoantigen-Specific T Cells

Another exciting application of neoantigens is in adoptive cell therapy (ACT), where T cells are isolated or purposefully engineered to target tumor-specific antigens. By isolating T cells that recognize neoantigens and expanding them ex vivo, researchers can create a potent army of tumor-fighting immune cells.

A groundbreaking study in Science⁷ highlighted the efficacy of neoantigen-specific T cells in treating metastatic colorectal cancer. Researchers identified neoantigens in patient tumors, isolated T cells that recognized these antigens, and infused them back into the patients. The therapy resulted in complete tumor regression in one patient and partial responses in others. This approach has since been extended to other cancers, including breast and ovarian cancer, with promising results. The ability to harness the immune system’s natural specificity for neoantigens makes ACT a highly adaptable and effective strategy.

Combination Therapies

Neoantigen-based therapies are increasingly being explored in combination with other immunotherapies, such as immune checkpoint inhibitors (ICIs). ICIs, such as monoclonal antibodies that block inhibitory signals like PD-1 or CTLA-4, can enhance the activity of neoantigen-specific T cells.

A study published in Cell⁸ demonstrated that combining neoantigen cancer vaccines with anti-PD-1 therapy significantly improved outcomes in melanoma patients. The combination not only enhanced T-cell responses but also led to a higher rate of complete responses compared to either therapy alone.

Such combination strategies hold immense potential for overcoming resistance to single-agent therapies and improving long-term outcomes for cancer patients.

Challenges in Neoantigen-Based Cancer Immunotherapies

Despite their promise, neoantigen-based therapies face several challenges:

Tumor Heterogeneity

Tumors are often composed of multiple subclones, each with distinct mutations. This heterogeneity can limit the effectiveness of therapies targeting a single neoantigen.

Challenging Identification and Validation

Accurately predicting and validating neoantigens remains a complex and resource-intensive process. This requires advanced genomic and bioinformatics tools to accurately predict which mutations will generate effective neoantigens.

Manufacturing Complexity

Personalized cancer therapies require rapid turnaround times, posing logistical and financial challenges.

Immune Evasion

Tumors can develop mechanisms to evade immune detection, such as downregulating MHC expression or acquiring additional mutations⁹.

Addressing these challenges will require continued innovation in next-generation sequencing technologies, bioinformatics, and manufacturing process development.

Future Directions

The field of neoantigen research is rapidly evolving, empowered by the strengths of genomic sequencing for cancer treatment, with several exciting developments on the horizon. Recent advancements in AI-driven neoantigen prediction involve the development of machine learning algorithms aimed at enhancing the accuracy and efficiency of neoantigen identification. Additionally, researchers are exploring the potential of off-the-shelf neoantigen vaccines that target shared neoantigens common among multiple patients. This approach could simplify vaccine production and accessibility. Furthermore, there is ongoing research into the role of neoantigens beyond cancer, with a focus on non-mutational neoantigens that could have applications in the treatment of infectious diseases and autoimmune disorders¹⁰.

Conclusions

Neoantigen discovery and validation have revolutionized cancer immunotherapy, offering unprecedented levels of personalization and specificity. From cancer vaccines to adoptive cell therapies, their clinical applications are transforming the way we treat cancer. While challenges remain, ongoing advancements in technology and research, particularly in genomic sequencing for cancer treatment, are paving the way for even greater breakthroughs.

At GenScript, we are committed to offering a comprehensive one-stop solution for customized neoantigen peptide synthesis, catering to every step of your research journey. Our research-grade and cGMP-compliant neoantigen peptide manufacturing services can fully support your needs from early-stage screenings and preclinical to clinical studies.

Relevant Resources

Reference

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• 3. Sahin U., & Türeci Ö., (2018). Personalized vaccines for cancer immunotherapy. Science. https://doi.org/10.1126/science.aar7112
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• 5. Hilf N., et al. (2019). Actively personalized vaccination trial for newly diagnosed glioblastoma. Nature. https://doi.org/10.1038/s41586-018-0810-y
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