A new brain-mapping neurotechnology called Single Transcriptome Assisted Rabies Tracing (START) combines two technologies—monosynaptic rabies virus tracing and single-cell transcriptomics—to map the brain’s neuronal connections with precision.
The method identified transcriptomic cell types and found that local cortical circuit connectivity is transcriptomic subclass and subtype specific. Using the technique, researchers at the Salk became the first to identify the patterns of connectivity made by transcriptomic subtypes of inhibitory neurons in the cerebral cortex.
Having the ability to map the connectivity of neuronal subtypes could lead to the development of novel therapeutics 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.
This work is published in Neuron, in the paper, “Transcriptomic cell-type specificity of local cortical circuits.” This is the first to resolve cortical connectivity at the resolution of transcriptomic cell types.
Neuronal functions rely on networks of diverse excitatory and inhibitory neurons. Although some local connectivity rules between major neuronal subclasses have been established, the information about connections at the level of transcriptomic subtypes remains unclear.
“When it comes to treating neurological and neuropsychiatric disorders, we’ve essentially been trying to fix a machine without fully understanding its parts,” said Edward Callaway, PhD, professor at Salk. “START is helping us create a detailed blueprint of the brain’s many parts and how they all connect.”
To create START, the Callaway lab combined monosynaptic rabies tracing and single-nuclei RNA sequencing to identify transcriptomic cell types and define neuron populations. The approach lets a modified virus move from one cell type of interest to cells directly connected to it.
The researchers first used START to explore connectivity patterns in the mouse visual cortex. START was able to resolve around 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 across 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’re actually very diverse, and trying to study or clinically target them as one group can obscure important differences that are critical to brain function and disease,” said Maribel Patiño, PhD, 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. Each subtype’s unique connectivity helps establish sophisticated microcircuits that likely contribute to specialized brain functions.
More specifically, the authors noted that using START, they could transcriptomically characterize “inhibitory neurons providing monosynaptic input to five different layer-specific excitatory cortical neuron populations in mouse primary visual cortex (V1).” And, at the subclass level, they “observe results consistent with findings from prior studies that resolve neuronal subclasses using antibody staining, transgenic mouse lines, and morphological reconstruction.”
For example, the researchers were able to resolve the inhibitory subtype Sst Chodl cells, which are thought to be associated with sleep regulation. They found that Chodl cells were the cell type most densely connected to layer 6 excitatory neurons, which are known to project to the thalamus to coordinate sleep rhythms.
The researchers’ next steps are to create viral vectors and gene-editing technologies that target each individual cell subtype. In the future, these tools could be adapted into novel therapeutics that selectively modify the specific neuron populations contributing to conditions such as autism, Rett syndrome, and schizophrenia.
“We don’t know exactly how this information is going to be used 10 or 20 years from now, but what we do know is that technologies are changing rapidly, and the way the brain is treated today with drugs is not the way the brain will be treated in the future,” said Callaway. “START can help drive this innovation, so the viruses and resources are all freely available for the entire neuroscience community to use.”
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