Finding the Best Tumor Antigen Peptides for Immunotherapy

Immunotherapy has been a game-changer for treating solid tumors. By harnessing and strengthening the body’s immune defenses, these treatments allow our immune cells to better recognize and target tumor cells for elimination. Some immunotherapy strategies take advantage of neoantigens to develop vaccines or T cell therapies.

  • “Tumor-Specific antigens are derived from completely new proteins formed by indels, translocations, or other mutations and thus provide greater potential for immunogenicity.”

    Julie Rumble, Ph.D.,

    Cayman Chemical

Julie Rumble, Ph.D.

What Are Neoantigens?

You may immediately recognize the prefix “neo” derived from Greek neos meaning “new” or “novel.” Tumor neoantigens are just that, new antigens.

How do they come to exist? One major mechanism for their formation is the genomic instability typical of cancer cells. Increased mutational burden means that cancer cells may express proteins, not typically present in normal tissues or just simply having the wrong sequence. Within tumors, new protein sequences not expressed anywhere else in the body are great candidates for immunotherapy.

  • “By focusing on patients that are responding to their tumor, we are able to identify T cell receptors (TCRs) and targets that enable tumor elimination”

    Marvin Gee, Ph.D.,


Marvin Gee, Ph.D.

How Neoantigens Elicit An Immune Response?

T cell responses are at the center of neoantigen-based immunotherapies.

Neoantigens must be presented by MHC molecules to induce an immune response.  MHC presentation means that neoantigens are accessible for T cell recognition (CD8+ and CD4+ T cells) and have the potential to trigger activation and T cell expansion.

  • “Multiple factors are contributing to the neoantigen’s role in personalized immunotherapy.”

    Michael Zhou, Ph.D.,


Michael Zhou, Ph.D.

Why Are Neoantigens Used in Cancer Immunotherapy?

Neoantigens are considered as non-self, thus more immunogenic.

Neoantigens are highly individual/cancer-specific and unlikely to escape from central tolerance.

TCRs might recognize certain neoantigens to accelerate adoptive T cell therapies.

  • “with any given cell line there may be a 10 fold range of how much MHC is expressed in the same number of cells, we frequently recommend starting with at least 100 million cells or 100 mg of dry tumor weight”

    Julie Rumble, Ph.D.,

    Cayman Chemical

Julie Rumble, Ph.D.

How Are Neoantigens Isolated?

Your workflow starts at the tumor site for identifying neoantigens.

Once you have isolated tumor cells and processed them for purification of MHC-bound peptides, mass analysis (i.e., LC-MS/MS) combined with the use of databases will allow you to identify a number of tumor antigen peptides.

Whether these tumor-derived proteins are in fact neoantigens and immunogenic enough can only be demonstrated by in vitro testing.

Neoantigens Must Be Validated.

To validate neoantigens, you may rely on different in vitro methods. For example, proteins with sequences of interest may be overexpressed for validation of MHC I peptides.

Alternatively, you may choose to incubate cells with synthetic soluble peptides allowing direct MHC I presentation.

For MHC II peptides the in vitro approach is different, as you will want to ensure protein uptake by phagocytosis for endolysosomal processing.


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