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NeoGenomics, Biognosys Partner to Flesh Out Proteomics Offerings for Pharma Market

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NEW YORK — With their recently announced global strategic partnership, clinical lab and research firm NeoGenomics and Swiss proteomics firm Biognosys aim to address increasing interest among pharmaceutical clients in proteomics and spatial biology tools.

At the core of the partnership is the combination of Biognosys' mass spectrometry-based proteomics workflows and NeoGenomics' MultiOmyx spatial proteomics platform. The companies presented data at the American Association for Cancer Research meeting this month on research using these technologies to identify protein biomarkers that could predict response to immunotherapy in melanoma patients.

In that work, researchers from Schlieren, Switzerland-based Biognosys used the company's data-independent acquisition mass spec workflow, TrueDiscovery, to profile formalin-fixed paraffin-embedded samples from 15 melanoma patients characterized at three months after immunotherapy treatment as either responders (nine) or non-responders (six). The same samples were also analyzed via NeoGenomics' MultiOmyx, which allows for measurement of dozens of proteins targets in their spatial context.

The mass spec assays identified 76 proteins that were differentially regulated between the two groups, while the MultiOmyx work identified 11 proteins and various immune cell components that distinguished between responders and non-responders.

Anna Juncker-Jensen, principal scientist and associate director of academic collaborations at NeoGenomics, said that the two approaches can potentially bring complementary data to questions in immuno-oncology and pharma research more generally. She noted, for instance, that the mass spec-based proteomics workflow identified a number of protein pathway signatures that proved informative, while the MultiOmyx platform added the spatial and immune phenotyping data that is increasingly valued, particularly in immuno-oncology research.

The MultiOmyx system was originally developed by GE Healthcare and was offered as a service through the company's Clarient Diagnostic Services division. The platform uses antibodies conjugated to fluorescent dyes to stain proteins of interest in batches of two analytes at a time. Researchers then image the stained tissue and deactivate the fluorescent dyes via a proprietary process. They can then stain the tissue with the next round of antibodies, multiplexing in an iterative fashion.

NeoGenomics acquired Clarient in 2015, and it offers its pharma clients a range of technologies including next-generation sequencing, flow cytometry, and spatial biology tools.

"We never want to have to turn any study down for the lack of having an assay," Juncker-Jensen said. She noted that proteomics was an area where the company lacked offerings, which led it to explore a relationship with Biognosys.

The partnership actually began several years ago, said Kristina Beeler, chief business officer at Biognosys. The COVID-19 pandemic delayed its efforts, though, she said. The AACR work represents the first data the two companies have presented from their collaboration.

For Biognosys, the collaboration provides access to the fast-growing spatial proteomics space, an area where it has not traditionally played.

"Especially in the immuno-oncology space, people are very interested in [spatial information]," Beeler said. "Is it an immune cell, is it a cancer cell that is expressing a marker? This was one of the synergies that we saw in this relationship. Spatial resolution is not something that we can provide. So there is a nice complementarity to the two technologies."

Beeler said the collaboration was part of a larger effort at Biognosys to make proteomics a more mainstream tool in pharma research and to make it a more routinely used technology in clinical trials. She said that the technology had advanced in areas like reproducibility, throughput, costs, and sample requirements to where it was ready for wider uptake.

"In the early days of the commercial activity of our company, unbiased mass spec was really used mainly by early adopters in R&D settings doing small-scale studies," she said. "What we have seen in the last few years is pull from the market to incorporate proteomics in the clinical [research and trial] space, and to combine it in a multiomics, multimodal approach."

Biognosys announced in January that it had received good clinical practice compliance and good laboratory practice certification for its proteomics research facility, developments that stemmed from work the company has being doing with drugmaker Roche on incorporating proteomics into clinical trials.

Beeler said that within the clinical trial space, the company is seeing two major areas of demand for its proteomics tools — using unbiased assays for exploratory protein biomarker studies and developing targeted panels to inform clinical decisions. She cited recent work done with drugmaker Kymera, under which the company used its targeted proteomics platform to generate pharmacodynamic markers that were used in a clinical trial.

"There is a lot of buzz around proteomics right now," said Juncker-Jensen. She said that particularly in the case of pharma research involving clinical samples, making the most of a limited amount of sample is a key priority, which makes proteomics attractive given its ability to measure thousands of proteins in a small amount of tissue.

"Anything multiplex in that space has an advantage," she said.

Multiplexing also appears to be on the rise in the spatial proteomics space, with companies including Akoya Biosciences, Standard BioTools, Bruker, and NanoString Technologies all offering or working on systems that can multiplex 100 or more proteins in a spatial context. NeoGenomics has multiplexed as many as 60 markers on the MultiOmyx platform, but Juncker-Jensen said most analyses using the platform look at around 10 to 30 markers, and she doesn't anticipate significant demand for higher levels of multiplexing.

Instead, she said, among its pharma customers, NeoGenomics is seeing demand for faster run times and the ability to run small batches of samples.

"People want to run two or three samples because accrual is slow and they need information right now," she said. "We might typically wait until we had a batch of 20 [samples], but now everything moves so fast that people can't wait."

In addition to the MultiOmyx platform, NeoGenomics offers high-throughput spatial proteomics on Akoya Biosciences' PhenoImager HT, which can multiplex up to six markers per sample in around 300 samples per week.

Juncker-Jensen said the company took a platform agnostic approach and would consider new spatial proteomics technologies as they emerged, but noted that the company has "spent a lot of years optimizing and perfecting the MultiOmyx workflow."

"We're open to onboarding new technologies if we feel like there is a gap in our offerings," she said. "But we have a good platform that is already running very smoothly."

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