Droplet microfluidics has revolutionized single-cell RNA sequencing, offering a low-cost, high-throughput method for single-cell genomics. However, this method has been limited in its ability to capture complete RNA transcription information. In a study published yesterday in Nature Methods, researchers have come up with an elegant, low-cost method that solves that problem. And not only does it push single-cell genomics forward, but it may also allow for new avenues for studies of infection and immune biology.
In 2015, researchers from Harvard University and the Massachusetts Institute of Technology introduced Drop-seq, a method to simultaneously and efficiently characterize the identities of thousands of cells, using nanoliter-scale droplets and attaching a unique identifier to each cell's RNA.
"Those technologies are very popular because they've lowered the cost of these types of analyses and sort of democratized them, made them very cheap and easy to do for many labs," says Iwijin De Vlaminck of Cornell University. The drawback, however, is that they can only identify a certain type of mRNA molecule, which limits the potential scope of analyses.
De Vlaminck and his collaborators have come up with a simple, inexpensive twist to the existing Drop-seq protocol. They call their new method DART-seq (droplet-assisted RNA targeting by single-cell sequencing).
In Drop-seq, individual cells are encapsulated with labeled microparticles that initiate reverse transcription of cellular mRNA. The De Vlaminck group devised an effective method to enzymatically customize the beads prior to performing conventional Drop-seq analysis, which allows for the recovery and analysis of a greater variety of molecules than are available through Drop-seq sequencing.
In addition, this technology can identify virus-infected cells and quantify viral and host gene expression, thus enabling examination of the host response to infection at single-cell level.
"A single virus species can be very diverse, and that diversity permits them to do extraordinary things," says co–lead author Philip Burnham. "So if you can zoom down to the single-cell level, you can actually see how minor changes in the virus cause a potentially huge change in how the cell reacts to that small mutation."
Co–lead author Mridusmita Saikia thinks DART-seq will also help inform new approaches to cancer therapy.
"Cancer cells are a very heterogeneous population," she says, "and when you don't look at them at the single-cell level, you often miss important information. So our technology also allows that."