Personalized Cancer Treatment: Immuno-Peptidomics and MS Reveal the Secrets of Tumor Neoantigens

The study of Immunopeptidomics focuses on exploring all peptides related to the antigen presentation process. These peptides play an essential role in both cell-mediated and humoral response-mediated immunogenic epitopes. Immunopeptidome refers to the study of the complete set of peptides presented on MHC I or II molecules participating in the antigen presentation pathway of nucleated cells. They are crucial for exploring cell-mediated and humoral response-mediated immunogenic epitopes. Immunopeptidome analysis is a qualitative and quantitative analysis of MHC I class and MHC II class immune peptides, which can not only identify targets for personalized cancer immunotherapy (such as tumor-specific mutation neoantigens or tumor-associated antigens) but also help develop new peptide vaccines and immune cell therapies. In recent years, with the innovation of proteomic technology and the continuous advancement of cell immunotherapy, Immunopeptidomics has been strongly promoted and developed.

 

Neoantigens, a type of antigen encoded by tumor-specific mutant genes, are an important member of immunopeptides with broad application prospects. These neoantigens are mainly present in the form of point mutations, expressed only in tumor tissues, and not manifested in normal tissue cells. T cells that specifically bind to neoantigens are exempt from thymus negative screening, so neoantigens have less destructive activity to normal tissues, have a high degree of tumor specificity and less non-target toxicity. Therefore, neoantigens are broadly considered as ideal therapeutic targets in tumor therapy.

 

Neoantigens can be divided into two types based on the type of MHC molecules, namely MHC I neoantigens and MHC II neoantigens. MHC I neoantigens are usually short, consisting of 8-13 amino acids and mainly derived from endogenous proteins. In contrast, MHC II neoantigens are usually longer, consisting of 13-22 amino acids and mainly derived from exogenous proteins. After a series of processing and presentation processes within the cell, the mutant genes in the tumor cells are transcribed into mRNA and translated into the corresponding mutant proteins. These abnormal proteins are degraded by the proteasome into a large number of peptides and bind to the HLA (Human MHC) molecules in the tumor cells. Subsequently, these peptides are presented on the surface of tumor cells. Some of the mutant peptides can be recognized by the T cell receptor (TCR), triggering an immune response and exerting a tumor immune killing effect. These mutant peptide segments that exist only in tumor cells and can be specifically recognized by T cells are referred to as "neoantigens".

 

Advantages of Mass Spectrometry Detection of Immunopeptides and Neoantigens

The identification and screening of neoantigens are one of the key elements based on the immunotherapy of neoantigens. By using the immune purification technology to enrich the immunopeptides bound to MHC in situ, and using mass spectrometry analysis technology to resolve the amino acid composition of immunopeptides, the positive rate of neoantigen screening can be significantly improved. The mass spectrometry analysis method can capture the immunopeptides that have been processed and presented at the amino acid level, significantly reducing the errors caused by traditional antigen presentation prediction methods.

 

The Main Steps of Neoantigen Screening Based on Mass Spectrometry Strategy

1. Immunopurify MHC binding peptides.

2. Use liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to finely separate and analyze MHC binding peptides, and obtain mass spectrometry data.

3. Establish a user-customized protein sequence database, including mutant proteins and standard human proteins.

4. With the help of proteomic analysis software (such as PEAKS, Mascot, pFind, MaxQuant, etc.), the mass spectrometry data are searched in the sequence database to identify potential immunopeptide segments that bind to MHC.

5. Use computer-aided methods (such as predicting the binding affinity of MHC and immunopeptide segments) to screen candidate peptide segments.

6. Carry out in vitro immuogenicity validation of the immunopeptide segments screened by the computer, and finally confirm the effective tumor neoantigens. This method based on mass spectrometry technology can accurately and efficiently identify and screen neoantigens that bind to MHC, providing important information and basis for personalized tumor treatment.

 

Applications of Immunopeptidomics

With the increasing attention in the application of mass spectrometry in the identification of tumor neoantigens. Proteomic technology based on mass spectrometry is the only method that can directly determine tumor neoantigens at the amino acid level. Neoantigens have broad application prospects in cancer treatment, mainly reflected in the following three aspects:

 

1. Immune Cell Therapy

By isolating and purifying immune T cells that can specifically recognize neoantigens from patients' tumor tissues or peripheral blood, immune cells with stronger anticancer ability and fewer side effects can be obtained. Compared with ordinary TIL cells or CIK cells, these immune cells have a stronger killing effect on tumors.

 

2. Tumor Neoantigen Vaccine

The neoantigen vaccine is a method of effectively stimulating, enhancing, and diversifying anti-tumor T cell responses. By using peptide synthesis technology to obtain neoantigens and prepare neoantigen vaccines, specific T cell immune responses can be stimulated in patients, thereby exerting a tumor killing effect. The neoantigen vaccine has the advantages of simple preparation, high feasibility, and high overall safety.

 

3. Combination with Other Tumor Treatment Methods

The application of neoantigens can improve the treatment effect of tumor patients based on PD-1 inhibitor therapy. Although anti-CTLA-4 and anti-PD-1 antibodies have achieved good results in melanoma patients, they also come with some side effects. However, some patients share some neoantigen peptide segments generated by somatic mutations, and these shared neoantigens can promote tumor immune responses, making CTLA-4 checkpoint therapy more effective in melanoma patients.

 

Through the above application methods, mass spectrometry detection of immunopeptides provides important support and guidance for the research and application of tumor neoantigens.

 

One-Stop Solution for Neoantigen Discovery

MtoZ Biolabs's one-stop solution for neoantigen discovery provides services including peptide synthesis, functional screening of neoantigen candidates for individualized cancer vaccines and T cell therapies, animal tests for individualized cancer vaccines, and immunogenicity tests for vaccines in the clinical stage.

 

Results Delivery

1. A List of All Identified Immunopeptides, Neoantigen Peptides, and Tumor-Related Antigen Peptides

2. Quality Analysis of Immunopeptidome Data, Such as Data Reports in Research Cases