A new tool provides speedy analysis of gene expression patterns in individual neurons from postmortem brain tissue. Researchers have used the method to compare the genetic signatures of more than 3,000 neurons from distant brain regions.
Scientists typically use a technique called RNA-Seq to measure gene expression in neurons isolated from postmortem brains. However, analyzing the data from this approach is daunting because the analysis must be done one cell at a time.
The new method combines RNA-Seq with software that allows researchers to analyze the expression patterns of thousands of neurons at once1. The investigators described the automated technique, called single-nucleus RNA sequencing (SNS), in June in Science.
The researchers tested the method on postmortem brain tissue from a 51-year-old woman with no known neurological illnesses. They used a laser to dissect 3,227 neurons from six brain areas, including those involved in language, cognition, vision and social behavior. They then performed RNA-Seq on the cells, getting a readout for RNAs produced in each cell.
The software identifies genes by matching a short segment of each RNA to a gene on a reference map of the human genome. The researchers then quantified each gene’s expression level.
The process correctly identified the subtypes of 2,253 neurons that ramp up brain activity and 972 neurons that dampen it.
Within these two broad classes, the neurons fell into 16 groups based on their location and their origin in the developing brain. For example, neurons from the visual cortex show different patterns of gene expression than do neurons from the temporal cortex, which processes hearing and language.
The findings expand the list of features that distinguish neurons from other cells in the brain. Researchers could use the method to identify patterns of gene expression in the brains of people with autism.