Conceptual image of blue neurons with glowing segments over blue background.
Conceptual image of blue neurons with glowing segments over blue background.

CRACK Method Reveals Novel Neuron Type in Mouse Brain

A new technique reveals cells’ precise locations and functions in the brain. Its developers have already used it to identify a previously unknown neuron type.

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Dan Robitzski

Dan is a Staff Writer and Editor at The Scientist. He typically works on the news desk and joined the team in 2021. He has a background in neuroscience and earned his master's in science journalism at New York University.

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Apr 18, 2022

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Neuroscientists examining a brain cell typically have to choose between studying its internal molecular activity or detailing its connections and electrical activation in the brain. But in his lab at Boston University, biologist and biomedical engineer Jerry Chen has developed a technique that allows researchers to do both, mapping neurons within a living mouse’s brain and then assessing their gene expression.

The new technique, called comprehensive readout of activity and cell type markers (CRACK), combines calcium imaging microscopy with a variation on a DNA labeling approach called hybridization chain reaction–fluorescence in situ hybridization (HCR-FISH) to label and track mRNA. CRACK allows researchers to first observe the electrical firing of neurons in the brain of a live mouse during a behavioral task, and then track the expression of specific genes in slices of the animal’s brain, ultimately linking specific cells and their molecular activities to particular behaviors. 

“There was a technology gap that required marrying molecular information [from existing databases] with the functional information” from behavioral studies that his lab focuses on, Chen tells The Scientist. Prior to CRACK, researchers could only monitor the neural activity of one cell type at a time, Chen explains, and there was no feasible way to connect that activity to the molecular workings going on inside those cells because obtaining each type of information required separate experiments.

The paper describes how the team used CRACK to identify a previously overlooked neuron type, the Baz1a cell, in the primary somatosensory cortex of the mouse brain. According to Chen’s findings, Baz1a cells help coordinate neural activity related to learning in response to tactile sensations on mouse whiskers. Chen says that even though they created CRACK for this specific experiment, they’ve just scratched the surface of how the methodology could be used. 

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Illustration showing how calcium imaging and HCR-FISH combined is a technique called comprehensive readout of activity and cell type markers (CRACK)
ONE-STOP SHOP: First, calcium imaging provides precise neural microscopy data on the arrangement and activity of individual cells within the brain of a live mouse. Then, hybridization chain reaction–fluorescence in situ hybridization (HCR-FISH) on tissue samples yields information on the expression of specific genes of interest. Combining these imaging methodologies into a technique called comprehensive readout of activity and cell type markers (CRACK), allows researchers to elucidate a cell’s type, conne
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“Now, if you have a tissue of a thousand neurons, you can actually start to label all eleven, twelve, thirteen, fourteen, fifteen different types of neurons that we know exist,” Chen says. “Then you can ask: How does cell type A communicate with cell type B?” Chen envisions several possible uses for CRACK, including studying the neural function of species beyond mice and humans for which tailored neuroscience tools may not be available, or answering “any question that involves trying to marry molecular information with dynamics—functional information” on the behavior of neurons.

University of California, San Diego, neuroscientist Takaki Komiyama tells The Scientist that the main benefit of the technique is being able to “define the expression of dozens of genes in a given neuron.” With CRACK, “you can record hundreds of neurons’ activity and pretty precisely identify the cell type of each of those hundreds of neurons,” adds Komiyama, who didn’t work on the paper but helped pioneer the use of calcium imaging over the past two decades.

Komiyama notes that “it’s a very specialized approach” and “takes a lot of manual practice,” but speculates that CRACK could spread as members of Chen’s lab train visiting scholars and other researchers, not unlike the way calcium imaging has “become so common” after labs such as Komiyama’s introduced it in 1997. 

This article was featured in April 2022, Issue 2 of the digest