How Sensory Experiences Shape Neurons

Summary: A new study presents BARseq, a rapid and cost-effective method for mapping brain cells, revealing new insights into how our brains are structured at the cellular level. Researchers used BARseq to classify millions of neurons in multiple mouse brains, discovering unique “cellular signatures” that define each brain region.

The study also highlighted how sensory deprivation, such as loss of vision, can significantly reorganize these neural structures, highlighting the importance of sensory experiences in shaping the brain. This new tool not only advances our understanding of brain architecture, but also opens possibilities for exploring brain changes associated with disease.


  1. BARseq technology enables rapid and extensive mapping of neurons in the brain, identifying distinct cellular signatures unique to each brain region.
  2. Sensory experiences, particularly vision, play a critical role in maintaining and forming the distinct cellular identities of different brain areas.
  3. The BARseq method is both more affordable and faster than previous brain mapping technologies, allowing researchers to conduct advanced studies of the brain.

Source: Allen Institute

Scientists have long known that our brains are organized into specialized areas, each responsible for distinct tasks. For example, the visual cortex processes what we see, while the motor cortex governs movement. But how how these regions form – and how their neural building blocks differ – remains a mystery.

A study published today in Nature sheds new light on the cellular landscape of the brain. Researchers at the Allen Institute for Brain Science used an advanced method called BARseq to quickly classify and map millions of neurons in nine mouse brains.

They discovered that even though brain regions share the same types of neurons, the specific combination of these cells gives each area a distinct “signature,” similar to a cellular identity card.

The team then explored how sensory input influences these cellular signatures. They found that the sight-deprived mice underwent a major reorganization of cell types within the visual cortex, which blurred distinctions from neighboring areas.

These changes were not limited to the visual area but occurred in half of the cortical regions, although to a lesser extent.

The study highlights the central role of sensory experiences in forming and maintaining the unique cellular identity of each brain region.

“BARseq allows us to see with unprecedented precision how sensory input affects brain development,” said Xiaoyin Chen, Ph.D., co-senior author of the study and an assistant research scientist at the Allen Institute.

“These vast changes illustrate the importance of vision in shaping our brains, even at the most basic level. »

A powerful new brain mapping tool

Previously, capturing single-cell data across multiple brains was a challenge, said Mara Rue, Ph.D., co-senior author and scientist at the Allen Institute. But BARseq is cheaper and less time-consuming than similar mapping technologies, she said, allowing researchers to examine and compare the molecular architecture of multiple individuals’ brains.

BARseq labels individual brain cells with unique RNA “barcodes” to track their connections in the brain. This data, combined with gene expression analysis, allows scientists to locate and identify large numbers of neurons in tissue slices.

For this study, researchers used BARseq as a standalone method to rapidly analyze gene expression in intact tissue samples. In just three weeks, researchers mapped more than 9 million cells from eight brains.

The scale and speed of BARseq provides scientists with a powerful new tool to delve deeper into the intricacies of the brain, Chen said.

“BARseq allows us to move beyond mapping what a ‘model’ or ‘standard’ brain looks like and start using it as a tool to understand how brains change and vary,” Chen said . “With this throughput, we can now ask these questions in a very systematic way, which is unthinkable with other techniques.”

Chen and Rue pointed out that the BARseq method is freely available. They hope their study will encourage other researchers to use it to study the organizing principles of the brain or focus on cell types associated with disease.

“This is not something that only big labs can do,” Rue said. “Our study is a proof of principle that BARseq allows a broad range of people in the field to use spatial transcriptomics to answer their own questions.”

About this news about brain mapping and neurotechnology research

Author: Pierre Kim
Source: Allen Institute
Contact: Peter Kim – Allen Institute
Picture: Image is credited to Neuroscience News

Original research: Free access.
“In situ whole-cortex sequencing reveals input-dependent area identity” by Xiaoyin Chen et al. Nature


In situ sequencing of the entire cortex reveals input-dependent area identity

The cerebral cortex is composed of neuronal types with diverse gene expression and organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture, connectivity, and neuronal activity, are connected in modular networks.

However, it remains to be determined whether these spatial organizations are reflected in neuronal transcriptomic signatures and how these signatures are established during development.

Here, we used BARseq, a high-throughput in situ sequencing technique, to interrogate the expression of 104 cell type marker genes in 10.3 million cells, including 4,194,658 cortical neurons across nine forebrain hemispheres of mouse, at cellular resolution. De novo clustering of gene expression in single neurons revealed transcriptomic types consistent with previous single-cell RNA sequencing studies. The composition of transcriptomic types is highly predictive of cortical area identity.

Furthermore, areas with similar compositions of transcriptomic types, which we defined as cortical modules, overlap with highly connected areas, suggesting that the same modular organization is reflected in both transcriptomic signatures and connectivity. .

To explore how the transcriptomic profiles of cortical neurons are developmentally dependent, we assessed the distribution of cell types after neonatal binocular enucleation.

Notably, binocular enucleation caused cell type composition profiles to shift from visual areas to neighboring cortical areas within the same module, suggesting that peripheral inputs sharpen the distinct transcriptomic identities of areas within cortical modules.

With the high throughput, low cost, and reproducibility of BARseq, our study provides proof of principle for using large-scale in situ sequencing to reveal brain-wide molecular architecture and understand its development.

News Source :
Gn Health

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