Genomic recording systems to reveal evolutionary modifications in primate neocortex

Project Summary/Abstract Primate brains develop following an exquisitely conserved Bauplan that is shared with other mammals, yet also possess advanced cognitive capabilities. These capabilities manifest from innovations to cellular and molecular repertoires, but the developmental origin of these evolutionary modifications has remained elusive due to lack

of tools that enable access to primate neurodevelopmental processes. A major evolutionary modification is the expansion of the neocortex. Within the neocortex, areas associated with higher-order cognitive functions (and their disorders) have expanded disproportionately relative to areas that process sensory information. The

increase in cortical territory devoted to higher-order processing has been accompanied by fundamental differences in neocortical cell type composition (the absolute and relative proportions of different cell types), gene expression, and cell-cell connectivity properties. For example, unlike sensory areas, higher-order areas

are typified by long-range connectivity to other higher-order areas. Mechanisms for the establishment of primary sensory areas and their connectivity have been worked out in mice, but it is not known whether these rules are conserved in primates, especially in expanded higher-order neocortex which lacks a rodent homolog.

Thus, we lack understanding of when and why higher-order areas establish their unique cellular characteristics and come to disproportionately connect to each other to form the long-range networks in primate brains. This proposal seeks to address this gap by applying modern molecular tools and genomic analyses to discover

rules for the development and connectivity of sensory and higher order areas in the common marmoset, an emerging and genetically tractable primate model species. Cellular lineage tracing methods delivered in utero to developing marmosets will be paired with single cell RNA and DNA sequencing to reconstruct lineage

relationships and progenitor population demographics across sensory and higher order areas. Lineage- resolved spatial sequencing will determine how clonal dispersion statistics differ between primary sensory and higher-order areas, and between marmosets and mice. Emerging technologies for reconstructing the

connections between individual cells, such as those based on barcoded, synapse-transiting viruses, will reveal how and when connectivity is established across brain areas. Marmosets offer distinct advantages for this program, including a high-quality genome, small size, and rapid sexual maturity, while retaining primate-

specific brain features such as expanded higher-order cortex and long-range connectivity. This research program leverages the power of quantitative genomic measurement and cell type-resolved recording technologies to reconstruct the developmental and evolutionary histories of primate brain specializations. The

knowledge and expertise gained by developing this expanded toolbox will improve access to developmental processes in non-traditional model species broadly. It will also be foundational for the development and assessment of NHP preclinical models for genetic perturbations that affect brain development.