Multiomic atlas of the developing thalamus reveals how neuronal identities emerge

A team from the Institute for Neurosciences (IN), a joint center of the Spanish National Research Council (CSIC) and Miguel Hernández University of Elche (UMH), has developed the first multiomic atlas of the mouse embryonic thalamus, providing a detailed reconstruction of how the different neuronal cell types in this brain region emerge during development.

Published in Nature Neuroscience, the study reveals that sensory neurons and those involved in motor and associative functions follow distinct developmental trajectories from very early stages. The researchers also identify the gene Sp9 as an essential regulator of the proper establishment of visual neuron identity.

The thalamus is a key brain structure that not only relays information to the cerebral cortex but also integrates sensory signals and contributes to the organization of sensory maps. Over the past few years, the Development, Plasticity and Reprogramming of Sensory Circuits laboratory, led by researcher Guillermina López-Bendito at the IN CSIC-UMH, has helped shed light on this active role of the thalamus.

This brain region is made up of distinct nuclei, each containing groups of neurons specialized in sensory, motor and associative functions. However, questions remain about how these nuclei form during embryonic development and what determines the identity of their neurons. In this study, collaboration with José López-Atalaya, head of the Cellular Plasticity and Neuropathology laboratory at the IN CSIC-UMH, has made it possible to reconstruct the developmental trajectories of these cells and identify the genetic programs involved in their differentiation.

An atlas to reconstruct thalamic development

To investigate how the different types of thalamic neurons form, the team used a single-cell approach to analyze individual cells from the embryonic mouse brain at different stages of development. This atlas has enabled them to trace the developmental trajectories of thousands of neurons, from their earliest stages to their final specialization.

The team analyzed each cell individually to determine which genes were active and identify which regions of DNA were accessible for gene regulation. “By integrating these two layers of information, we were able to reconstruct how cells differentiate over time and identify the gene regulatory programs that control these trajectories,” explains López-Atalaya.

One of the study’s main findings is that thalamic neurons do not follow a single path toward specialization. The data reveal two major cell lineages that diverge very early during embryonic development: one gives rise to sensory nuclei, while the other forms nuclei associated with motor and associative functions. In addition, the two genetic programs progress at different rates, with sensory circuits reaching certain developmental stages earlier than those involved in cognitive and motor functions.

The team also discovered an unexpected intermediate stage within the sensory pathway: before specializing, some neurons pass through a molecular state resembling that of neurons that form the higher-order nuclei of the thalamus. Unlike first-order nuclei, which relay sensory information from the outside world, such as visual or tactile signals, to the cerebral cortex, higher-order nuclei participate in more complex communication circuits between brain regions.

To confirm that the cells followed this trajectory, the researchers used a genetic labeling technique that allowed them to track the fate of progenitor cells and the neurons they generate. “This enabled us to experimentally validate the relationships between cells that we had predicted and discover that, within the sensory lineage, cells first pass through a state resembling that of higher-order nuclei before becoming sensory neurons, such as visual or somatosensory neurons,” explains Lorenzo Puche-Aroca, first author of the study.

SP9, a key transcription factor in visual neuron identity

Building on the genetic programs identified in the atlas, the team found that the gene Sp9, which contains the instructions for producing the SP9 protein, a transcription factor that regulates the activity of other genes, is essential for certain thalamic neurons to acquire their specific visual identity. To investigate its role, the researchers experimentally reduced its activity during mouse embryonic development.

“We wanted to go a step further and determine whether these genes actually played a role in neuronal specialization. When we reduced Sp9 activity, we found that visual neurons did not properly acquire their identity. This shows that this gene plays a key role in establishing the characteristics that distinguish these neurons during development,” explains López-Bendito.

The findings provide a new resource for studying how the thalamus is organized during development and how its circuits and functions are established. This knowledge offers a framework for better understanding certain alterations that may be associated with neurodevelopmental disorders and neurological diseases.

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Robert Egan

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