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.”
Canine connection
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
Calviri Tries New Approach to Cancer Dx, Vaccines With Frameshift Peptides | GenomeWeb
