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MD Anderson, IsoPlexis Link T-Cell Functionality to Immunotherapy Response in AML

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NEW YORK (GenomeWeb) – Researchers from MD Anderson Cancer Center and single-cell proteomics firm IsoPlexis have found that T-cell cytokine production is linked to response to immunotherapy in leukemia patients.

In a study presented this month at the American Association for Cancer Research annual meeting, the researchers found that a measure of T-cell functionality called PSI (polyfunctional strength index) strongly predicted response to the combination of nivolumab (marketed by Bristol-Myers Squibb as Opdivo) and azacytidine (marketed by Celgene as Vidaza) in  a set of 10 patients with relapsed acute myeloid leukemia (AML).

They also found in an analysis of 26 new and relapsed AML patients that T-cell functionality was significantly impaired in relapsed patients and patients with the TP53 mutation compared to newly diagnosed, wildtype patients. TP53 mutations are linked to an increased risk of cancer and to adverse outcomes in cancer patients.

The researchers measured T-cell functionality with IsoPlexis' IsoCode platform, which enables single-cell protein measurements. Using the platform, they measured the levels of 32 cytokines secreted by patient T-cells, calculating patient PSI scores based on the level of cytokines expressed by their T-cells. PSI was defined as the percentage of polyfunctional T-cells (cells secreting more than one cytokine) in a given patient sample multiplied by the intensities of the secreted cytokines.

Naval Daver, associate professor at MD Anderson and first author on the study, said that he and his colleagues struck up their collaboration with IsoPlexis as part of an investigation into potential biomarkers for AML patient response to the nivolumab-azacytidine combo.

"We were seeing some encouraging responses, but we didn't have a very good biomarker to identify who were the patients who were exhibiting those good responses," Daver said.

The researchers used a variety of approaches including immunohistochemistry, flow cytometry, and RNA-seq to identify potential markers of response but were also interested in looking at T-cell cytokine profiles, as cytokine production is often associated with T-cell fitness and immune response, he said.

They began with a small pilot study, sending pre-treatment bone marrow samples from responders and non-responders to IsoPlexis for analysis, finding that the two groups could clearly be distinguished by their PSI scores.

They then ran the 26 samples from new and relapsed AML patients on the platform to determine how their PSI scores correlated with the diagnoses. Of particular interest was whether the TP53 mutation would impact immune status.

The hope, Daver said, was that TP53 mutations would not affect immune function, which might indicate that immunotherapies could be a good tool for attacking cancers with this mutation.

"Unfortunately, however, it seems that TP53 has a broad impact not only on the molecular signal but also on the immune signal," he said.

Daver said he and his colleagues are now collecting additional patients from the nivolumab-azacytidine to test whether PSI distinguished between responders and non-responders in larger cohorts.

The researchers are also investigating how PSI scores change in response to treatment.

"We would expect that the PSI [of responders] would go up further [post-treatment], which would be a good indicator of a clinical response being associated with a favorable immune biology," Daver said.

He said the researchers are also looking at the extent to which PSI is predictive of response to immunotherapies specifically versus a more broadly prognostic measure of a patient's immune health.

"That's something we don't know yet," he said. "We're looking at that, sending [IsoPlexis] samples of patients who got other [treatments] and non-immune therapies to figure out if it has similar predictive value. Hopefully this could just be a marker [indicating] that these patients have preserved immune function and will have a better chance of response to other cytotoxic therapies."

For IsoPlexis, the study is a move into the checkpoint inhibitor space after a number of publications and collaborations focused on chimeric antigen receptor (CAR) T cell therapy.

The Branford, Connecticut-based company's IsoCode platform uses microchips featuring arrays of thousands of microchambers that isolate individual cells from samples of interest. These chambers are then sealed with a slide patterned with groups of antibodies in a number of different spatially isolated lines. This allows the researchers to identify proteins based on the color of fluorescence produced upon binding and the location on the slide where the binding event occurs. In this way, they can multiplex well beyond the levels allowed by fluorescence readout alone.

The company was spun out of the lab of Rong Fan, associated professor of biomedical engineering at Yale University and is based on technology originally developed in the lab of California Institute of Technology researcher James Heath, where Fan was a postdoc.

Last year, IsoPlexis launched its IsoLight platform, an automated analysis system that it has placed in 22 research centers worldwide, according to CEO and Co-founder Sean Mackay.

He said that while many of the system's early adopters are focused on CART therapy, the company is now making inroads into other types of immunotherapies and treatments, as evidenced by the MD Anderson project.

Currently, IsoPlexis is focused on T-cell cytokine analysis, but it plans to move into different classes of cells and molecules with the launch of several new products this year, including panels for measuring polyfunctional strength of immune cells as well as for measuring qualities of innate and myeloid. The company is also developing panels for measuring metabolomic and phosphoproteomic markers at the single-cell level.

Phosphoproteomics figured into an early demonstration of Isoplexis' technology in a 2016 paper published in Cancer Cell in which Heath's lab used the approach to analyze the response of glioblastoma cells to drug treatment, identifying phosphoproteomic changes indicative of emerging resistance as early as 2.5 days after treatment.

IsoPlexis raised $13.5 million in Series B funding in 2017 to support development of its technology and is planning to raise additional funds in the near future to help further build out its commercialization efforts, MacKay said, though he declined to say how much it was targeting.

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