New Method Enables Efficient scRNA-seq of Individual Samples

Researchers at École polytechnique fédérale de Lausanne (EFPL) in Switzerland have applied machine-vision and co-encapsulation to tailor single-cell RNA sequencing (scRNA-seq) to individual samples, an advance that could expand its use in patient biopsies. 

scRNA-seq allows scientists to study the expression of genes in an individual cell within a mixed population. It involves capturing the RNA of a single cell and, after multiple molecular conversion reactions, sequencing it. Since RNA is the intermediate step from DNA to protein, it provides an overview about which genes in that particular cell are active and which are not.

Because scRNA-seq captures the activity of all genes in the cell’s genome, it has become the gold standard for defining cell states and phenotypes. It has also been widely adopted in medical and pharmacological research because it can identify which cells are actively dividing in a tissue or which are reacting to a particular drug or treatment. “These single-cell approaches have transformed our ability to resolve cellular properties across systems,” says Professor Bart Deplancke at EPFL’s School of Life Sciences. “The problem is that they are currently tailored toward large cell inputs.”

In fact, scRNA-seq requires over a thousand cells for a useful measurement. “This renders them inefficient and costly when processing small, individual samples such as small tissues or patient biopsies, which tends to be resolved by loading bulk samples, yielding confounded mosaic cell population read-outs,” says Dr. Johannes Bues, a researcher in Deplancke’s group.

To address this, the team developed a method that allows scRNA-seq to efficiently process samples with fewer cells. Dubbed “deterministic, mRNA-capture bead and cell co-encapsulation dropleting system, or DisCo for short, the technique uses machine-vision to actively detect cells and capture them in droplets of oil and beads. Precise particle and cell positioning and droplet sorting control allows for continuous processing of low-input single cell suspensions at over 70% capture efficiency at speeds that can reach 350 cells per hour.

To further showcase DisCo’s unique capabilities, the researchers tested it on the small chemosensory organs of the Drosophila fruit fly, as well as on individual intestinal crypts and organoids. The researchers used DisCo to analyze individual intestinal organoids at different developmental stages. The approach detected various distinct organoid subtypes, some of which had never been identified before.

“Our work demonstrates the unique ability of DisCo to provide high-resolution snapshots of cellular heterogeneity in small, individual tissues,” says Deplancke.

The findings were published recently in Nature Methods.