Magnetic beads map gene expression in single cells

Newly developed microscopic beads give cells unique barcodes based on the cells’ gene expression patterns. This faster and cheaper system could help researchers study autism in cultured cells.

By Maris Fessenden
25 March 2015 | 3 min read
This article is more than five years old.
Neuroscience—and science in general—is constantly evolving, so older articles may contain information or theories that have been reevaluated since their original publication date.

Unique profiles: A heat map shows the number of unique messenger RNA strands per gene per cell, a measure of diversity in gene expression across cells.

Investigators have deployed microscopic magnetic beads to measure gene expression in individual cells. This faster and cheaper system, described 6 February in Science, could help researchers study autism in cultured cells1.

Scientists typically measure gene expression using one of two methods. Flow cytometry works in single cells for a relatively small number of genes. By contrast, DNA microarrays profile a vast quantity of genes in a pooled sample. A third technique, called microfluidics, marries cellular specificity with scope, but is pricey and laborious.

For the new method, researchers developed an attractive way to capture and read a cell’s messenger RNA (mRNA) — the single-stranded copies of genes that serve as blueprints for protein production. Together, these mRNA molecules provide a snapshot of gene expression within the cell.

To snag mRNA, the researchers drop a single cell into a tiny well filled with nutrient-rich fluid. Each well gets a microscopic magnetic bead studded with several hundred million genetic probes that snap onto specific pieces of mRNA.

Each genetic probe also contains a sequence that indicates which bead it is attached to, and another sequence that is unique to the probe itself. Together, these sequences form a barcode that distinguishes each mRNA from an individual cell.

The researchers chemically pry open the cells, releasing their mRNA into the fluid — to be ensnared by the probe-covered bead. After 10 minutes, they pluck out the beads using a magnet, strip the mRNA-probes and sequence the genetic material. A customized computer program uses the barcodes to organize the sequencing information, providing a readout of gene expression in each cell.

In the study, the researchers tested the system on human blood cells. They probed the expression of 98 genes, some of which are notoriously difficult to analyze using flow cytometry because they are expressed inside the cell, rather than on the outside where florescent probes can mark them. The researchers identified specialized cells that have large effects on the sample’s overall gene expression patterns despite representing less than 0.1 percent of the total cell population.

This finding highlights the importance of studying large numbers of single cells, the researchers say.

When exposed to a virus, the cells’ gene expression patterns responded to the immune challenge, confirming that the system shows shifts in these patterns in response to certain events.

As developed, the beads can handle gene expression from just a few thousand cells, but increasing the size of the wells and the number of probes on the beads could boost that cell limit. The cost of the method is estimated at less than $1 per cell — which the researchers say is much cheaper than for microfluidics systems. Scientists may be able to purchase the system starting in late 2015.


1. Fan H.C. et al. Science 347, 1258367 (2015) PubMed