New brain mapping tool could be the “BEGINNING” of next-generation therapies

Salk Institute scientists unveil a new brain-mapping neurotechnology called single transcriptome-assisted rabies tracing (START). This cutting-edge tool combines two advanced technologies – monosynaptic rabies virus tracing and single-cell transcriptomics – to map the brain’s complex neuronal connections with unparalleled precision.

Using this technique, researchers became the first to identify connectivity patterns created by transcriptomic subtypes of inhibitory neurons in the cerebral cortex. They claim that this ability to map the connectivity of neuronal subtypes will promote the development of new treatments that can target certain neurons and circuits with greater specificity. Such treatments could be more effective and produce fewer side effects than current pharmacological approaches.

The study, published in Neuronis the first to resolve cortical connectivity at transcriptomic cell type resolution.

“When it comes to treating neurological and neuropsychiatric disorders, we are essentially trying to repair a machine without fully understanding its components,” says lead author Edward Callaway, professor and Vincent J. Coates Chair of Molecular Neurobiology. in Salk. “START helps us create a detailed map of the many parts of the brain and how they all connect.”

It’s like trying to repair a car without knowing what an engine or an axle is, he said. But if you had a diagram of the car’s parts, you could begin to understand how they could work together to turn the wheels and make the car move. This knowledge would then make it much easier to spot a problem in the system and determine what tools you would need to resolve it.

When describing the parts of a brain, neurons are initially grouped into two broad classes: excitatory (those that stimulate brain activity) and inhibitory (those that suppress activity), such as accelerator and brake. ‘a car. From there, they can be classified into subclasses: excitatory neurons are classified based on the layer of the brain they are found in, while inhibitory neurons are identified by the marker proteins they express.

Recent advances in transcriptomics now make it possible to break down these subclasses even further. Using single-cell RNA sequencing, scientists can now group cells with similar gene expression patterns and define each group as a specific neuronal subtype.

“Defining a cell type is complicated because you can group cells differently depending on the method you use to examine them,” Callaway says. “Two cells might have slightly different gene expression patterns but perform a similar function, or two cells with similar gene expression might be further separated based on their anatomy, connectivity, or physiology. If you only consider One of these features you might end up dividing or subdividing the groups START helps us understand what level of categorization may be most meaningful for circuit function, and this will indicate which cells to target with new treatments. .

To create START, the Callaway lab designed a way to combine single-cell RNA sequencing with another previously developed technique: monosynaptic rabies virus tracing. The approach allows a modified virus to jump from a cell type of interest to only those cells that are directly connected to it. By detecting where the virus ends up, researchers can map which cells are connected to which cells.

The researchers first used their new tool to explore connectivity patterns in the mouse visual cortex. START was able to resolve approximately 50 different subtypes of inhibitory neurons in this region and map their connections to excitatory neurons in each layer of the cortex. The researchers’ findings identified distinct connectivity patterns in various transcriptomic subtypes of inhibitory neurons that could not have been distinguished using previous methods.

“People often treat all inhibitory neurons as a single uniform group, but they are actually very diverse, and trying to study or target them clinically as a single group can mask important differences that are essential to brain function and functions. diseases”, explains the first author, Maribel. Patiño, a former graduate student in Callaway’s lab and current psychiatry resident at UC San Diego School of Medicine.

START revealed that each cortical layer of excitatory neurons received selective input from specific transcriptomic subtypes of Sst, Pvalb, Vip, and Lamp5 inhibitory cells. The unique connectivity of each subtype helps establish sophisticated microcircuits that may contribute to specialized brain functions.

For example, researchers were able to resolve an inhibitory subtype called Sst Chodl cells, which are thought to be associated with sleep regulation. Using START, they found that Chodl cells were the cell type most densely connected to layer 6 excitatory neurons, known to project to the thalamus to coordinate sleep rhythms.

This unprecedented resolution will allow neuroscientists to continue to uncover how specific neuronal subtypes shape brain circuits to produce our thoughts, perceptions, emotions and behaviors.

The researchers’ next steps are to create viral vectors and gene-editing technologies targeting each individual cell subtype. In the future, these tools could be adapted for new treatments that selectively modify specific neuronal populations contributing to pathologies such as autism, Rett syndrome and schizophrenia.

“We don’t know exactly how this information will be used in 10 or 20 years, but what we do know is that technologies are changing rapidly and the way the brain is treated today with drugs is not the one whose brain is being treated will be treated in the future,” Callaway says. “START can help drive this innovation, so that viruses and resources are all freely available to the entire neuroscience community.”

Other authors include Marley A. Rossa, Willian Nuñez Lagos, and Neelakshi S. Patne of the Salk Institute.