Developmental barcoding and lineage mapping of the brain in neurotypical mice and mouse models of autism

  • Awarded: 2019
  • Award Type: Bridge to Independence
  • Award #: 606178

The foundation for the functional and anatomical complexity of the brain is laid during embryogenesis, when the neural plate develops into the entire central nervous system in a series of increasingly complex differentiation, migration and patterning events. These events have been coarsely mapped to describe the developmental histories of certain brain regions and neuronal subtypes. However, unlike other tissues, in the brain, each neuron assumes a potentially unique functional identity and connectivity profile. As such, more detailed and comprehensive lineage maps, ones with single-neuron resolution, would allow for a more comprehensive understanding of the brain’s development and how it relates to its connectivity, cognitive functions and aberrations in neurodevelopmental conditions, such as autism. Obtaining such developmental maps is challenging due to the breadth of the information that needs to be recorded. Current methods lack either the throughput or the resolution required to address this level of complexity.

To address these challenges, Reza Kalhor will build upon his prior experience with mouse barcoding and in situ sequencing technologies1,2 in order to create in vivo developmental barcoding maps of the mouse brain. Such an approach will involve the use of mouse models that carry genomic loci, which randomly alter their sequence to create a unique and heritable DNA signature. As these unique signatures accumulate in cells during development, they combine to create barcodes that embody the cell’s lineage history.

Kalhor also aims to address the challenges associated with readout of these barcodes from individual neurons without losing anatomical and positional information. To approach this objective, he will establish droplet-based and in situ single-cell sequencing technologies to obtain lineage maps at a single-neuron resolution. Once established, he will implement these barcoding and barcode readout strategies in neurotypical and a variety of autism spectrum disorder (ASD) genetic mouse models, including Chd8, Cntnap2 and Mecp2 knockout mice, to compare their embryonic brain development. The creation of these detailed maps will aid in our understanding of what goes awry during development in ASD and will further our ability to classify distinct ASD subtypes.


1.Kalhor R. et al. Nat. Methods 14, 195-200 (2017) PubMed
2.Kalhor R. et al. Science 361, eaat9804 (2018) PubMed
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