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Vision is the result of light being detected and transduced into neural signals by the retina of the eye. This information is then further analyzed and interpreted by the brain. First, light enters the front of the eye and is focused by the cornea and lens onto the retina—a thin sheet of neural tissue lining the back of the eye. Because of refraction through the convex lens of the eye, images are projected onto the retina upside-down and reversed.
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Light enters the eye through the cornea, a transparent, dome-shaped surface covering the surface of the eyeball that helps to direct and focus incoming light. This light is then channeled toward the pupil, an adjustable opening whose size is controlled by the iris. The iris, a pigmented muscle, regulates the amount of light entering the eye by contracting or dilating the pupil, thereby ensuring optimal light levels for clear vision.
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Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual

Fangming Xie1,2, Saumya Jain1,3,2, Runzhe Xu1,2

  • 1Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

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|January 8, 2024
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Summary
This summary is machine-generated.

Early visual experience shapes mammalian brain development by altering neuronal gene expression. This study reveals how vision influences layer 2/3 cell types in the visual cortex during critical developmental periods.

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Area of Science:

  • Neuroscience
  • Developmental Biology
  • Genomics

Background:

  • Early sensory experience is crucial for brain development, particularly during critical periods.
  • The organization of neuronal cell types in the mammalian neocortex is influenced by postnatal sensory input.
  • Layer 2/3 (L2/3) glutamatergic neurons are key sites for experience-dependent plasticity and learning in the cortex.

Purpose of the Study:

  • To investigate how visual experience affects the spatial organization and molecular profiles of L2/3 cell types in the primary visual cortex (V1).
  • To understand the transcriptomic changes in L2/3 neurons induced by visual deprivation.
  • To elucidate the mechanisms by which vision patterns cortical cell types during postnatal development.

Main Methods:

  • Spatial transcriptomic profiling of L2/3 cell types in V1 using approximately 500 genes.
  • Application of multi-tasking theory to model gene expression profiles as a 2D manifold.
  • Comparison of transcriptomic data from normally reared and dark-reared mice.
  • Integration of spatial transcriptomic data with single-nucleus RNA-seq data.

Main Results:

  • Spatial transcriptomics revealed the zonation of L2/3 cell types along the pial-ventricular axis in V1.
  • Visual deprivation induced two independent gene expression programs: one affecting cell state (orthogonal to cell type) and another altering cell type identity.
  • Visual deprivation shifted the distribution of L2/3 cells within a transcriptomic continuum, decreasing B-type and C-type cells while increasing A-type cells.
  • The spatial organization of L2/3 cell types is linked to continuous gene expression profiles represented as a 2D manifold.

Conclusions:

  • Visual experience critically shapes the organization and identity of L2/3 cortical cell types during postnatal development.
  • Visual deprivation leads to distinct transcriptomic changes, impacting both cell state and cell type composition.
  • The findings provide insights into how sensory experience sculpts neural circuits, influencing brain wiring, function, and behavior.