NEW YORK – Calviri is investigating the use of immunogenic protein fragments called frameshift peptides (FSPs) as a new class of diagnostic biomarkers and targets for vaccine response.
The Phoenix-based company recently published the results of a Phase I feasibility study on using FSPs to predict immune checkpoint inhibitor (ICI) response in lung cancers in the Journal of Translational Medicine.
Calviri is also currently conducting three other Phase I FSP studies: two using the markers for early stage breast and colorectal cancers and another using them as therapeutic molecules for the treatment of renal medullary carcinoma.
Additionally, the company has several preclinical efforts underway in other indications, including canine applications.
Frameshift peptides are short amino acid chains found at the ends (generally at the C-terminus) of frameshift neoantigens (FSNs), which arise from RNA processing errors such as exon skipping during splicing. These neoantigens trigger the production of antibodies, which can be detected and identified using an FSP array.
"We discovered that there was a treasure trove of tumor cell states that lead to aberrant peptides at the C-terminus of normal proteins and that aren't found in healthy cells," said Kathryn Sykes, VP of research and product development at Calviri.
Because these peptides represent targetable sequences and can elicit highly immunogenic responses, Sykes and her colleagues at Calviri saw potential for multiple uses in the cancer field.
"We really felt that the field is ready for new approaches to diagnosing, treating, and preventing cancer," she said.
In the recently published study, Calviri scientists took biobanked, pre-treatment serum samples from 74 patients with advanced lung cancers. Most — 86 percent — had non-small cell lung cancer (NSCLC) while the remainder had small cell lung cancer (SCLC).
FSP-antibody interactions were analyzed on custom chips and associations between treatment response, immune-related adverse events, and individual FSP profiles were calculated. From these data, the group built four models of response prediction and one model to predict adverse events. The different response prediction models were built to make predictions for all patients with nonzero scores, patients without stable disease, those receiving ICI monotherapy, and for those specifically with NSCLC.
Response prediction models showed between 93.8 percent and 100 percent accuracy, while the adverse event model demonstrated 90 percent accuracy.
"We were able to extract enough information from about 80 percent of the samples to apply our test," said Sykes. "Once applied, the tests predict therapy outcomes with very high accuracy."
"It's a preliminary tool but appears to have promise as a biomarker of [therapy] response," said Nina Bhardwaj, a professor of medicine whose research has focused on FSPs at the Icahn School of Medicine at Mount Sinai.
Bhardwaj, who was not involved with the study, added that its results "will definitely need to be validated in larger cohorts."
Sykes said that Calviri currently plans to conduct larger prospective studies of its predictive biomarker and vaccine efforts, both in lung cancers and in other indications. The firm has already collected some pediatric brain and renal medullary cancer samples for studies it aims to launch later this year.
The antibody binding assay used to detect these frameshift peptides occurs on a proprietary silicon chip, which was diced into 13 slides, each displaying 374,084 peptides.
This FSP chip is Calviri's key hardware.
While the chip used in the feasibility study contains all predicted FSP sequences, in order to discover those relevant to a disease state, Sykes said that future commercial offerings will consist of pared-down versions containing only those peptides relevant to the assay in question.
"We envision manufacturing chips and developing the FSP chip assay workflow into a turnkey system that could be used in CLIA or reference labs," she said. "Once developed, we envision licensing the manufacturing to a partnering company that holds expertise in scaled chip manufacturing. They might run the assays themselves or have other labs do it. Meanwhile, we would continue to innovate expanded FSP chips and improved workflows."
To that eventual end, Calviri is currently working to redesign the machine it uses for chip production.
"We are using pretty classical semiconductor industry photolithography," Sykes said. "We now have a team of engineers working on something completely different that might [enable] manufacturing on a different scale."
The goal, she added, is to be able to make "millions and millions of chips a year."
Although Calviri appears to be one of the very few companies, if not the only, developing FSPs for diagnostic and prognostic purposes, other firms have been developing FSPs as therapies, especially as potential cancer vaccines.
Switzerland-based Nouscom, for instance, is currently testing an off-the-shelf FSP immunotherapy called NOUS-209 and a personalized FSP-based cancer vaccine called NOUS-PEV. In addition to MSI-high colorectal cancer, gastric, and gastro-esophageal junction tumors, NOUS-209 is also being evaluated as a monotherapy for Lynch syndrome carriers in a separate Phase Ib study.
Calviri is also using its FSP platform to develop canine cancer vaccines and diagnostics. The company initiated a study of a vaccine for the eight most common canine cancers in 2019 and completed enrollment of 800 dogs last year.
"It's a lot easier to get a dog vaccine product through the [US Department of Agriculture]," Sykes said.
Proving that a cancer vaccine works in dogs, she explained, helps to convince others that such a vaccine may be feasible in humans.
"It's a way into the human market," Sykes said, while simultaneously a viable commercial product on its own.
Calviri is now preparing to submit a request to the USDA for a conditional license for its eight-cancer canine vaccine.
Dogs have made for an attractive cancer research model organism because their cancers more closely mimic those occurring in humans than do cancers in other model organisms such as mice. This has led to the growth of a cottage industry in canine cancer diagnostics and therapeutics.
Canine cancer firm One Health Company, for instance, markets a cancer screening test for dogs and has built a canine cancer database used to correlate the genomics, drugs, and outcomes relevant to canine cancer as an aid to cancer research in both dogs and humans.
VolitionRx and PetDx are also in various stages of canine cancer test development, with the former pursuing an ELISA-based blood test that identifies and measures circulating nucleosomes, and the latter developing a cell-free DNA-based test.
Sykes mentioned that Calviri's research into canine cancer diagnostics and vaccines has turned up other interesting results.
While the company's vaccine appears to reduce the incidence of cancer and of death due to cancer in dogs, it also appears to be reducing deaths from other chronic diseases as well.
"We don't know the mechanism yet," Sykes cautioned, however. "Talking with folks in the aging field, it seems most likely that we have a vaccine that [attacks] senescent cells."
Although Sykes said that Calviri has had some interesting conversations with scientists such as Harvard University's David Sinclair surrounding a potential senolytic vaccine, the company is not actively pursuing this line of research.
Calviri currently employs roughly 30 people and is going through a non-VC funding round.
The firm has been fundraising largely through existing investors and expects to raise enough money to fully launch its vaccine and diagnostic programs within the next six months.
"We've been very successful in engaging investors that are passionate and involved," Sykes said.