Researchers have developed a new technique that allows them to examine huge amounts of information from a single cell or zoom out and see data patterns among thousands upon thousands of cells — all in a single experiment. In work published Monday in the journal Nature Communications, scientists from the biotech company 10x genomics and Fred Hutchinson Cancer Research Center describe their method, which could help researchers dive deep into the ecosystem of cancer or other diseases.
The platform allows researchers to analyze which genes are turned on (and to what level) in tens of thousands of cells at once.
“What the technology allows you to do is to be able to identify different types of cells and how many there are, and also infer what they’re doing based on gene expression,” which could give researchers a better understanding of diseases such as leukemia, noted co-author Dr. Jerald Radich, a Fred Hutch physician-scientist who specializes in leukemia research.
Radich is working with the new technology to gain a better understanding of which cell types contribute to leukemia relapse. Once that’s understood, “you can imagine using it in the clinic as an adjunct to the ways that we look at residual disease [low levels of remaining leukemia cells that can contribute to relapse],” he said.
Fred Hutch’s Dr. Jason Bielas, the paper’s lead author, developed methods and designed the experiments needed to validate the platform, known as the Chromium Single Cell 3’ Solution. He and his team were able to analyze nearly 70,000 cells in a single experiment and use gene expression patterns to group individual cells by type.
Bielas also developed additional methods to detect subtle DNA variations and further expand the technology’s applications. Current methods to detect leukemic cells in patients often rely on surface markers. Using only gene expression information and slight differences in gene sequences, the team was able to distinguish between donor and recipient blood cells in patients who had received bone marrow transplants to treat their leukemia — an important component of patient care after transplant.
“We developed methods that we believe can be used to improve clinical care of cancer patients and save lives, in addition to addressing fundamental questions in biology,” said Bielas, who studies how errors in the genetic code contribute to disease and develops new technologies to address long-standing questions in mutation research.