ExSeq Combines Tissue Expansion with In Situ Sequencing to Improve Gene Expression Analysis

MIT and Harvard Medical School researchers have devised a way to label individual molecules of messenger RNA within a tissue sample and then sequence the RNA. This approach offers a unique snapshot of which genes are being expressed in different parts of a cell, and could allow scientists to learn much more about how gene expression is influenced by a cell's location or its interactions with nearby cells.

In a study appearing today in Science, the team showed that they could use this technique, called expansion sequencing (ExSeq), to locate and then sequence thousands of different messenger RNA molecules within the mouse brain and in human tumor samples.

ExSeq combines a novel method for expanding tissue with in situ RNA sequencing. Expanding the tissue before performing RNA sequencing has two main benefits: It offers a higher-resolution look at the RNA in cells, and it makes it easier to sequence those RNA molecules. Once the tissue is expanded, the researchers can label and sequence thousands of RNA molecules in a sample, at a resolution that allows them to pinpoint the molecules' locations not only within cells but within specific compartments such as dendrites.

Using an "untargeted" version of this technique, meaning that they are not looking for specific RNA sequences, the researchers can turn up thousands of different sequences. They estimate that in a given sample, they can sequence between 20 and 50 percent of all of the genes present.