New Tumor Mapping Tech Shows Potential to Make ‘Major Impact’ on Cancer Research

Nicolas Chevrier in his lab, which develops interdisciplinary approaches and tools to study how the immune system functions across biological scales.

A new technology developed at the University of Chicago has been recognized for its potential to make a major impact on basic and clinical cancer research.

Nicolas Chevrier, assistant professor of molecular engineering at the University of Chicago’s Pritzker School of Molecular Engineering, recently received the Duckworth Family Commercial Promise Award for his proposal, Spatiomolecular mapping of the tumor microenvironment.

The proposal was selected from a competitive pool of proposals and judged by a team from the University of Chicago Medicine Comprehensive Cancer Center (UCCCC) and the Polsky Center for Entrepreneurship and Innovation, as well as external experts. The review criteria included commercialization potential, investigators, innovation, scientific merit, as well as feasibility of milestones and future plans.

“Dr. Chevrier’s proposal for a spatial profiling platform demonstrated potential to make a major impact on basic and clinical cancer research. It will enable the analysis of the tumor microenvironment to yield new biomarkers for diagnosis and prognosis, candidate therapeutic targets, and fundamental insights about cancer biology,” said Kunle Odunsi, director of UChicago Medicine’s Comprehensive Cancer Center, dean for oncology, and the AbbVie Foundation Distinguished Service Professor.

Combining DNA microarrays and next-generation sequencing, the technology enables the processing of small-to-large samples ranging from a standard biopsy to whole-mount human organs or model organisms. A prototype of the platform outperformed the currently available commercial platform in all metrics tested, including sensitivity, surface area, resolution, and cost.

“One of the immediate uses of this could be studying the spatial features of tumors across large cohorts of cancer patients for the first time,” said Chevrier. “In doing so, you can look for features that correlate with better or worse outcomes.”

Moving forward, one goal is to make the platform compatible with archived biospecimens stored at hospitals, so the researchers can retroactively study large cohorts of patients with known outcomes. This would help determine why a certain drug didn’t work in a specific group of patients while working in others.

“Or maybe we can discover spatial molecular features of cancer lesions that were not known before because we’d now be able to look at many, many samples in a format that also allows for the analysis of the whole tumor as opposed to small biopsies only,” added Chevrier. “It could also be used to come up with new therapeutic targets that could be tested or investigated.”

With any of these use cases, Chevrier knew the technology could have a much broader application beyond his work in the lab. “That’s how we got here,” said Chevrier, who also cofounded Flexomics in 2019. The startup last month was awarded a two-year, $2 million Small Business Innovation Research grant from the National Human Genome Research Institute to further develop its core single-cell screening technology for new applications.

In his lab, Chevrier said they typically start with very basic questions – applying fundamental findings to further translational work.

The funding from the Commercial Promise Award will help focus the work related to the proposal “from a more translational angle from the start,” noted Chevrier. “In the future, we hope to work more and more with specimens from patients or human donors so that we can tie our fundamental studies more closely to things that can benefit patients.”

As for next steps, Chevrier said the immediate goal is to establish robust protocols for the platform so that it can be ready to be used as a commercial kit or as a service platform. He has established a collaboration with a partner in industry, Agilent Technologies, in support of this, and also is benefitting from a great collaboration with Ben Shogan, a gastrointestinal surgeon at UChicago Medicine to benchmark the technology on human colon cancer sections at the whole-organ level.

// University of Chicago Medical Center Trustee Tom Duckworth and his wife Connie in 2019 committed more than $1 million to establish the Duckworth Family Cancer Fund at UChicago Medicine, expanding the partnership between UCCCC and the Polsky Center.

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