Researchers have developed a powerful new method to map how brain cells are connected by tagging neurons with molecular ‘barcodes’. Using this technique, they were able to graph thousands of neural connections in the mouse brain with incredible speed and detail.
This method has the potential to improve our understanding of how complex brain networks are organized and how they function. It may also shed light on what’s wrong with neurological diseases and how diseases like Alzheimer’s disease develop over time.
“When you design a computer, you need to know the circuitry of the central processing unit. If you don’t know how everything is connected, you can’t understand how it works, you can’t optimize it, you can’t fix it when something breaks. We’re working the same way with the brain,” said Boxhuan Chao, a professor of cell and developmental biology at the University of Illinois at Urbana-Champaign, who led the study.
“Our technique allows us to simultaneously map thousands of neural connections at single-synapse resolution, a capability not present in any current technology. This has direct application to understanding circuit dysfunction in neurodegenerative diseases and could provide a platform for developing circuit-guided therapeutic interventions,” he said.
The research results were published in a magazine nature method.
How to map your brain faster and in more detail
Mapping the brain has traditionally been slow and difficult. Scientists often had to slice brain tissue into very thin sections, image them under a microscope, and piece together the pathways by hand. New sequencing-based tools can label many neurons at once, but they typically indicate where neurons extend, rather than identifying the exact cells they connect with at synapses, Zhao said.
To overcome this limitation, Zhao’s team created a new platform called Connectome-seq. Assign a unique RNA “barcode” to each neuron. Specialized proteins carry these barcodes from the body of the neuron to the synapse, the point where two neurons meet.
Researchers then isolate these synapses and use high-throughput sequencing to read which barcode pairs are found together. This reveals which neurons are directly connected, allowing scientists to map large-scale networks.
Rewire your brain into an ordering problem
“We transformed the neural connectivity problem into an ordering problem. Imagine a large bunch of balloons. The body of each balloon has its own barcode sticker across its entirety, and some travel down to the end of the string. If the two balloons are tied at the end, the two barcodes will touch at the junction,” Zhao said. “We then cut out the knots and arrange the barcodes for each knot. If the same knot has a balloon A and a balloon B sticker, we know these two balloons are tied together. We do this in the brain, at the level of just thousands of neuron cells. We can use this information to reconstruct sophisticated maps representing the connections between all these seemingly floating groups.”
Discover new brain circuit connections
Using Connectome-seq, the research team mapped more than 1,000 neurons in a mouse brain circuit that connects two brain regions, known as the pontocerebellar circuit. This analysis revealed previously unknown connectivity patterns, including direct connections between cell types not known to connect in the adult brain.
“We have already made improvements in our lab, and we are confident that we can continue to improve upon them and ultimately reach our goal of mapping the entire mouse brain,” Zhao said.
Potential to transform Alzheimer’s and brain disease research
Because Connectome-seq is fast and scalable, it has the potential to greatly accelerate research into neurodegenerative, psychiatric, and other brain diseases. Scientists may be able to identify early changes in neural circuits by comparing brain connections in healthy people with those in different stages of disease.
“The sequence-based approach has significantly reduced time and cost, allowing us to actually see the differences between different brains. We can now see where connectivity changes and where the most vulnerable parts of the brain are, perhaps before symptoms appear,” Zhao said. “For example, if we can pinpoint exactly where the weak links are that cause the devastating cascade of Alzheimer’s disease, could we specifically strengthen the connections where the disease slows or prevents progression?”
This research was supported by a Neuroomics Initiative grant from Stanford University’s Wu Tsai Institute for Neuroscience and funding from the Elsa U. Pardee Foundation and the Edward Mallinckrodt Jr. Foundation.
