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MIODx Aims to Develop Immune Repertoire Sequencing Assay to Predict Immunotherapy Response

SAN FRANCISCO (GenomeWeb) – MIODx is developing immune repertoire sequencing-based tests to predict whether patients will have a favorable response to immunotherapy and whether they will have adverse immune reactions as a result of the therapy. The San Jose, California-based company struck a development deal with DiaCarta this week and plans to eventually offer its assays as laboratory-developed tests out of DiaCarta's CLIA-certified laboratories in the San Francisco Bay Area and Nanjing, China.

MIODx Cofounder and Chief Operating Officer Sean Givens said that the firm has an "aggressive timeline" for commercialization and hopes to begin offering its assays in the first quarter of next year. In addition, Ellis said a longer-term strategy is to take the assays through US Food and Drug Administration clearance.

When MIODx — MIO stands for medically improved outcomes — first launched in 2014, it planned to develop a multiplexed PCR-based assay that analyzed DNA and RNA pathways that could predict whether a tumor would become metastatic. Its first planned product was a prostate cancer test and it raised $1.5 million in seed funding in 2016 to support the development.

However, Givens said, the company ran into complications obtaining clinical samples and began looking into whether it could apply its technology to easier-to-obtain analytes, like blood.

Then last year, it licensed technology developed in the University of California, San Francisco lab of Lawrence Fong related to immune repertoire sequencing. Fong heads the cancer immunotherapy program at UCSF and also serves on MIODx's science advisory board.

After that, Givens said, the company put its VerifyDx Prostate Cancer assay on hold. He added that the firm has validated VerifyDx and may look to license that technology out, but for now, it has "put all our efforts on developing the T cell receptor-based immuno-oncology test."

The goal now, Givens said, is to develop tests that can better predict who will respond to immunotherapy and who will have adverse outcomes. Immunotherapy has shown to be extremely successful in treating some cancers, with many patients' tumors essentially melting away. However, only around one-third of patients respond and "quite a few patients have severe immune adverse events," he said.

Givens said the company's assay would sequence the entire T cell receptor repertoire at the RNA level. Sequencing the entire repertoire is necessary to "truly understand what's going on, because it's super complex," he said. The technology licensed from UCSF is focused on the bioinformatics side — understanding the change in the immune repertoire before and during therapy.

The company started with Takara's SMARTer Human TCR profiling kit. Givens said it chose to work with that technology as the basis of its assay because it analyzes RNA rather than DNA. "We wanted to look at the functional repertoire," he said, so only the receptors that were being expressed. Then it modified the kit to include positive and negative synthetic RNA controls to make the assay quantitative and amenable to taking it through FDA clearance.

MIODx will look at a patient's immune repertoire at baseline before therapy has begun, and then again at various time points throughout treatment. It will then apply UCSF's algorithms to understand whether the change that is seen predicts a good response or an adverse immune reaction. "Basically, if there's a diverse reaction early on, with a diversity of clones, that predicts a better response," Givens said.

The goal is that the assay will be able to make these predictions early on in the course of treatment, so patients who are not responding can be taken off the therapy, saving them both time and money, Givens said. Similarly, the test may also predict that even if a patient's tumor will respond, there might also be adverse immune reactions. In that case, "the physician could potentially lower the dose, or administer steroids," Givens said, to prevent the adverse immune reaction without completely taking the patient off therapy.

The assay, ClonoMap, is now up and running and the company is working on clinical validation studies in collaboration with UCSF and other unnamed research institutions. It is also working with pharmaceutical companies that are interested in using the ClonoMap assay in its clinical trials to better stratify patients.

Givens said that by focusing on immunotherapy response and adverse immune reactions, MIODx aims to target a different market than immune sequencing firm Adaptive Biotechnologies, which markets both clinical and research immune repertoire sequencing assays. Adaptive's clinical assay, ClonoSeq, is mainly aimed at identifying minimal residual disease and predicting relapse in blood cancer patients and the company is working with Amgen to develop it into a diagnostic to predict minimal residual disease in acute lymphoblastic leukemia.

However, last year, Adaptive also struck a research agreement with the National Cancer Institute to use its technology to understand immunotherapy response.

In addition, other companies are also moving into the immune repertoire profiling space, including ArcherDx, which said last month that it would partner with Ambry Genetics to offer immune repertoire sequencing services to biopharmaceutical companies. Also, Thermo Fisher Scientific and Hudson Alpha Institute for Biotechnology spinout iRepertoire both offer immune repertoire profiling kits for research use.

"In terms of where we fit, we're hype- focused on immuno-oncology and trying to develop a test to predict immunotherapy response," Givens said, adding that the company's next steps are to continue to refine its algorithms and conduct clinical validation trials.