Cancer Vaccines: Using Neo-Antigen Peptide Array Screening

Immunotherapies have already shown startling effectiveness against certain previously intractable cancers and a pair of scientists were awarded this year’s Nobel Prize for their research into immune mechanisms known as checkpoint inhibitors. Yet, despite significant advances in cancer research, the disease continues to exact a devastating toll and while the best weapon against this implacable foe would be prevention, to date, this has been an elusive goal. However now, investigators at Arizona State University (ASU) have just described a new method for pinpointing tumor-specific factors in the blood that can elicit a protective immune response in the body and may one day be harnessed to produce an effective vaccine against the disease.

The new study outlines a means for rapidly identifying peptides produced by tumor-associated mutations, then screening these peptides to find those exhibiting a strong immune response. Findings from the study were published recently in Scientific Reports through an article titled “Using Frameshift Peptide Arrays for Cancer Neo-Antigens Screening.”

The technique described in the new study relies on libraries of peptides printed on slides known as peptide arrays. When such arrays are exposed to cancer-linked antigens in samples of patient blood, specific peptides bind with antibodies, suggesting they are recognized by the immune system and may be used in a vaccine against that cancer.

“Our system has the advantages of not requiring tumor tissue to DNA sequence and not having to guess whether a mutation elicits an immune response,” noted senior study investigator Stephen Johnston, Ph.D., a professor in the school of life sciences at ASU.

Results of the study indicate that tumor-associated peptide mutations not only bind with immune antibodies but can effectively provide cancer protection, at least in animal models of the disease. The peptides generating a strong immune response could be incorporated into a vaccine or alternatively, used in conjunction with other forms of immunotherapy to treat existing cancers.

The ASU researchers used peptide arrays to screen for tumor-linked peptides in blood samples from dogs, examining responses to nine different forms of cancer. The antigens showing the greatest immune response in the array were then evaluated for their protective effect against two forms of cancer, in a mouse model.

Results from the study confirmed that some of the peptides exhibiting a strong antibody response on the peptide arrays offered protection from cancer in mice, while non-immunogenic peptides did not.

Most efforts toward a cancer vaccine have focused on so-called point mutations. Such mutations occur when a single DNA nucleotide letter is replaced with a different nucleotide. For example, an original sequence of ACCTACA could mutate to form a sequence reading ACCTATA.

Point mutations, therefore, leave the sequence length unchanged, altering only the content of the DNA and resulting RNA transcripts. By contrast, frameshift mutations occur when sequence letters are inserted or deleted. (INDELS is the term for these insertion-deletion mutations.)

Currently, use of point mutations for experimental cancer vaccines has been largely based on algorithms that make predictions about which neoantigens will yield an effective immune response, which can only be tested for effectiveness once the vaccine has been manufactured. The process, which is estimated to take 1–3 months, is cumbersome, very expensive, and inaccurate. Use of frameshift peptide arrays could provide immediate information on peptide vaccine candidates and assess their immune reactivity before the formulation of vaccines.

In addition to indels, frameshift mutations can occur through a process known as exon mis-splicing. Exon splicing occurs prior to translation from RNA to protein. Nucleotide sequences known as introns, which do not code for proteins, are cut from sequences and ends of the remaining coding regions, known as exons, are fused. This process can mis-splice—either omitting part of the exon or including part of the unwanted intron sequence. Like INDEL mutations, exon mis-splicing is a rich source of immunogenic mutations, explored in the current research.

“We hypothesized that tumors may also generate frameshift peptides (FSPs) in transcription errors through INDELs in MS or by exon mis-splicing. Since there are a finite number of predictable sequences of such possible FSPs in the genome, we proposed that peptide arrays with all possible FSPs could be used to analyze antibody reactivity to FSPs in patient sera as an FS neo-antigen screen,” the authors wrote. “If this were the case it would facilitate finding common tumor neoantigens for cancer vaccines. Here we test this proposal using an array of 377 predicted FS antigens. The results of screening nine types of dog cancer sera indicated that cancer samples had significantly higher antibody responses against FSPs than noncancer samples.”

The authors went on to note that there are a finite number of possible peptides displaying frameshift mutations, so it is possible to construct arrays capable of interrogating the entire sequence space of these mutations, eventually establishing the most immunogenic candidates. A group of 10–20 such frameshift peptides could be used for an anticancer vaccine.

Subsequent testing of the frameshift peptides demonstrated that reactive peptides provided T cell protection from melanoma and breast cancer in mice, whereas nonreactive peptides offered no such protection. Intriguingly, this tumor protection directly correlated to the degree of antibody response to frameshift peptides seen in the array results.

The research paves the way for the development of potent new weapons against cancer, leveraging the body’s own immune defenses to stop this leading killer in its tracks.