Calviri’s approach can provide both cancer diagnostics and vaccines. It is based on the discovery of an unrecognized source of frameshift neoantigens. These immunogenic peptides are generated from very frequent errors in tumor-cell RNA synthesis and processing. They provide both cancer specific and shared frameshift neoantigens for a new class of diagnostic and vaccine products.

Science

Calviri’s approach is based on three key scientific insights and discoveries

  • Frameshift peptides are very immunogenic neoantigens and therefore very important for developing effective vaccines and diagnostics
  • Errors in RNA synthesis and processing by tumor cells are a far richer source of neoantigens than errors in DNA synthesis
  • Arrays of frameshift peptides can directly readout an individual’s immune responses to tumor neoantigens

In cancer patients, the immune system recognizes the frameshift neoantigens as foreign and antibodies are generated against them. A patient’s blood is applied to a microarray displaying peptides corresponding to all frameshift neoantigens that could be generated by errors occurring at the RNA synthesis and processing level. If antibodies from patients consistently bind to a set of arrayed-peptides, they may serve as a test to diagnose cancer. These neoantigen-peptides bound by patient antibodies can serve as compositions for both therapeutic and preventative vaccines.

RNA synthesis errors can lead to frameshifts that change the peptide sequence

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  • An mRNA is read by the translational machinery in groups, or frames, of 3 ribonucleotides at a time.
  • Each frame of 3 ribonucleotides defines a codon, and a codon recruits a specific amino acid to be added to a growing peptide chain.
  • Any mRNA synthesis error that shifts the translational reading frame changes the next codons, and hence changes the peptide sequence.
  • Errors can occur by insertions or deletions (indels), as shown here; however, RNA splicing errors are also common.

Tumor cells make many RNA synthesis errors, which generate many aberrant peptides

  • In normal cells, quality control mechanisms ensure that the products of nucleic acid synthesis are accurate and aberrant proteins are either repaired or removed quickly
  • In tumor cells, the activities of the quality control mechanisms are bypassed to enable faster cell growth
  • Since the error rate of RNA synthesis is 100s of times higher than that of DNA synthesis even in normal cells, the less controlled tumor cells make many RNA synthesis errors
  • In tumor cells many inaccurate RNAs are translated into many aberrant, frameshifted peptides and proteins; these are neither repaired nor removed

The aberrant peptides are neo-antigens, stimulating specific antibody production

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  • Tumor cells release the frameshifted peptides. These peptide variants are neo-antigens to the immune system
  • When a B cell and a helper T cell recognize a neoantigen, the B cell is activated
  • Activation leads to maturation into a plasma B cell that produces and secretes large quantities of antibodies that specifically recognize the neoantigen

Neo-antigens produced by a patient can be determined by probing a frameshift-peptide array with a small sample of their blood

  • The immune system recognizes the frameshift neoantigens as foreign, and antibodies are generated against them in cancer patients
  • A very small sample of blood can be applied to a microarray displaying all possible RNA-error generated frameshift peptides
  • Profiles of peptide binding activity determined to be associated with a cancer can serve as a diagnostic
  • Frameshift peptides bound by blood-antibodies in cancer patients can serve as compositions for both therapeutic and preventative vaccines

Applications

We have discovered that tumor cells make frequent and recurrent mistakes in RNA synthesis and processing that cause frameshift peptides (FSPs) to be produced. These peptide variants are released by tumor cells and recognized by the immune system, eliciting variant-specific antibodies. This rich source of immunogenic neoantigens has not been previously tapped. Frameshift neoantigens from RNA synthesis and processing errors are far more abundant than those from DNA replication errors. Calviri is taking advantage of this plentiful supply of immunogenic neoantigens to develop broadly useful Vaccines and Diagnostics against all cancers.

  • Microarrays carrying all possible RNA-synthesis frameshift error neo-peptides can be produced at scale.
  • A small amount of patient blood is applied to the microarrays which results in an antibody-based diagnostic for the early detection of cancer and companion products.
  • The neo-peptide diagnostic tests will be simple to conduct, and yield highly sensitive results.
  • The frameshift peptide arrays are used to identify those neo-peptides that recurrently bind antibodies in cancer patient blood.
  • Antibody binding activity to some neo-peptides is shared among patients with the same type of cancer; other binding activity is consistently shared among patients with different cancer types.
  • These shared, antibody-eliciting neo-peptides serve as neo-antigens to include in an inventory of off-the-shelf FAST (Frameshift Antigen Shared Therapeutic) Vaccines.
  • Clinical Studies are in progress to determine the potential impact of Prophylactic vaccines intended to prevent the occurrence of most major cancers. This includes the ongoing VACCS trials.
  • The same frameshift peptide arrays are used to identify collections of neo-peptides that collectively provide for blood-antibody binding activity profiles that span most major cancers.

Clinical Trials

Calviri is conducting the world’s largest canine cancer vaccine study to test the efficacy of a preventative vaccine against cancer. Human clinical trials in development include one for evaluating a pediatric brain cancer vaccine and a prognostic test for responders to checkpoint inhibitor immunotherapies.

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Norton, a 9 year old rat terrier mix receives one of the first vaccines in the Vaccinations Against Canine Cancer Study (VACCS)

  • Calviri is conducting the world’s largest canine vaccine study to test the efficacy of a preventative vaccine against cancer. Through the ASU Foundation and in collaboration with Colorado State University we are using a $6.4 M grant from Open Philanthropy Project to fund the vaccine study in dogs. This ongoing clinical cancer trial (VACCS) is testing a preventative vaccine to protect against all major cancers. A patent is filed on its composition.
  • Other dog vaccine trials in candidate discovery phase include ones for Hemangiosarcoma (HSA) and brain cancer.
  • Calviri has funding from the Gateway Foundation to conduct a therapeutic trial against pediatric DIPG brain cancer (diffuse intrinsic pontine glioma). Vaccine candidates have been discovered and selected for formulation.
  • In a collaborative trial with MD Anderson serum samples from cancer patients that received checkpoint inhibitor immunotherapy were tested on the frameshift peptide arrays. Results indicate that responders can be distinguished from non-responders. Additional patient samples have been collected to extend this effort toward a companion diagnostic for immunotherapeutic treatments.