Pattern in Brain
Credit: Rebus Biosystems

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To even begin to unravel the complex cell types in the brain, scientists seek ways to capture more expression from single cells, as well as their locations. That’s just what Lars Borm—PhD student in Sten Linnarsson’s lab at the Karolinska Institute in Sweden—wanted to do when he co-developed the Enhanced ELectric (EEL) FISH method.
Now, he’s working with Rebus to increase the automation and throughput of this method.

As Borm and his colleagues wrote, EEL FISH is “an smFISH-based method that combines high multiplexing with large area imaging at high resolution.” By combining this technique with the Rebus Esper, hundreds of genes can be tracked along with their spatial context. Borm needs such multiplexing as he studies some of nature’s most complex creations.

In mouse and human brains, Borm says, “There is a tremendous amount of complexity—on the order of hundreds to thousands of different cell types. And within a cell type, there are also tons of variation.”

To explore these highly structured tissues, Borm uses wide-field microscopy for its speed. Then, the EEL FISH method eliminates the need to image in the z-dimension by using electrophoresis to move the RNA to the surface of a sample, and does so accurately in terms of spatial organization. “There’s still a little bit of diffusion, but it is on the order of a few microns,” Borm says.

In addition to maintaining the spatial organization of the RNA, EEL FISH “dramatically cuts down the amount of imaging that is needed,” Borm explains. “Therefore, it increases the spatial throughput.” Consequently, it can be used on entire mouse brains and sections of human brains.

Expanding the applications

“Putting EEL FISH on the Esper platform will make the method run even faster,” according to Borm, who adds, “Their automation is nice.”  This combination of automation and speed, plus the Esper’s ease of use, will expand the applications of EEL FISH.
As an example, Borm says, “Human brain samples would be a perfect fit for the Esper system.”

Borm is especially interested in brain development. “I think the most interesting thing is patterning, seeing how the cells arrange themselves,” he continues. But that’s a complex process to study.

In the past, scientists explored brain development one transcription factor at a time. Putting EEL FISH on the Esper platform opens up completely new possibilities. “Now, in a single experiment, we can see what 200 or 400 transcription factors are doing,” Borm points out. “This complex information also requires a very complex analysis.” Although he believes that there is more information to extract from the data, he adds, “People are developing very nice analysis tools.”

EEL FISH simplifies some of that complexity. In human tissue, in particular, auto-fluorescent  lipofuscin granules in cells can drown out the RNA signals. EEL FISH removes about 90% of that unwanted material. “This is the first time anyone has done that at high resolution,” Borm says. “Removing everything that you don’t need reduces a lot of the background noise, making our signal much cleaner. That really enables us to study human samples, which is quite special.”

As a result, Borm envisions using EEL FISH in many ways on the Esper platform. As an example, the high resolution provides new opportunities to study neurodegenerative diseases. “I think there are many ways to apply this to Alzheimer’s and Parkinson’s to start,” according to Borm.

In the future, Borm hopes to scan full human brains at high resolution and single-cell accuracy of the RNA. But his ambitions don’t stop there. “If I can dream even bigger, I would do the whole body,” he says.


Learn more about the Rebus Esper.


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