UIC researchers receive $2.15M to develop cutting-edge method to study proteins in single cells

Researchers at the University of Illinois Chicago have received $2.15 million from the NIH’s National Institute of General Medical Sciences to develop methods for cutting-edge single-cell proteomics — the study of all proteins produced by an organism.

Spearheaded by Yu (Tom) Gao, associate professor in the Retzky College of Pharmacy, the project’s focus includes a platform that suspends individual cells in the air for analysis. This allows the researchers to evaluate the proteins produced by specific cells for proteomics.

With proteomics, researchers can gain different, deeper insights than with genomics, the study of genes, or transcriptomics, the study of the RNA they create. The proteins a cell produces perform actions within and among other cells in the body, so they provide the clearest picture of a cell’s real activity, said Gao.

“Ninety-nine percent of our biological functions are executed by proteins,” he said. “If the gene is the blueprint of life, the transcripts are the mold that make the parts, and the proteins are the final assembled car that you actually drive. When you want to see what’s wrong with the car, the most direct answer comes from investigating the car — the protein — itself.”

But unlike the nucleotides that make up genes and transcripts, proteins cannot be amplified to make them easier to study. And because analyzing the average of proteins from a bulk sample can cost nuances that have impact on how disease is treated, scientists have been trying to create ways to isolate proteins from individual cells instead.

For example, if 65% of cells in a breast cancer tumor are HER2 positive — a protein overexpression that makes them grow and divide quickly — while 35% are negative, bulk analysis will read the tumor as being HER2 positive. If clinicians prescribe HER2-destroying drugs, the 35% of tumor cells that are negative will remain untouched and multiply, said Gao.

“If we can measure the cells individually, we will know if even 0.01% of the cells are upregulated,” he said.

To address this, Gao’s team focused on protein sample loss. By levitating a cell in a special chamber, the researchers eliminated the possibility that some of the tiny sample gets left behind in or absorbed by the glass or plastic container used to contain the reaction. In their platform, which they named Levcell, all chemical reactions needed to extract protein from a cell are performed on it as it’s suspended in air.

“It’s very hard for the protein to escape from this droplet,” Gao said.

The researchers have automated all steps of the process, including sorting and probing of cells and mass spectrometry, the technique that identifies and quantifies proteins. They’ve successfully levitated a cell-containing droplet in the system for more than 72 hours continuously, and have invented a method of extracting single cells from tissues for use in the Levcell platform.

The grant funding will go toward refining methods so we can process up to 1,000 cells per day, Gao said. “Hopefully in the future we can drive down the cost to about $1 per cell.”

Long-term, they’re integrating AI tools that will use data gathered by the system to better guide sampling and screening.

And they’re putting the system to the test in real-world scenarios, collaborating with cancer researchers at UIC to probe circulating tumor cells. Clinicians are limited in the volume of blood they can extract from a patient for diagnostics, so using single-cell proteomics at a high sensitivity can boost the amount of diagnostic information they can get at one time, said Gao, who is a member of the University of Illinois Cancer Center.

“We want to drive single-cell proteomics into the affordable range, so researchers can utilize it to do more — including better diagnostics in cancer,” Gao said.