Complex brains have evolved to produce many diverse neuron types, yet the fundamental mechanisms of how diversity emerges during development remains largely elusive. New technologies allow us to infer developmental trajectory from single-cell sequencing data. To resolve the underlying cell-fating mechanisms, however, we need to pinpoint where and when a particular cell fate is established. To do this, we need sophisticated genetic tools to map the cell’s lineage.

The Lee lab uses both invertebrate and vertebrate model systems to study neuronal lineage development and fating mechanisms. Ultimately, we aim to tailor neuronal lineages to engineer neural networks with desired functions and to improve cell therapy for neurodegenerative diseases.

Drosophila melanogaster, the humble fruit fly, is a powerful genetic model that has recently emerged as a leading system to study brain development and function. The Lee lab has revealed the basic rules of fruit fly brain development. Each of the roughly 100 neural stems cells per brain hemisphere generates a unique, stereotyped lineage. The ~100 distinct lineages indicate that each neural stem cell is specified with its own lineage identity. The stem cells divide repeatedly to produce an invariant sequence of neurons, indicating a birth-order or temporal fating mechanism.

Thanks to our understanding of lineage identity, we were able to target specific Drosophila neural stem cells for molecular profiling. We profiled selected time points to reveal temporal dynamic genes. This helped identify two RNA-binding proteins expressed in opposite temporal gradients in all cycling neural stem cells. These gradients promote early versus late temporal fates and govern stem cell aging. In rapidly changing neuronal lineages, however, we found these long-range gradients dispensable for many aspects of birth-order dependent fate specification. We are therefore in search of parallel temporal fating mechanisms. We also want to use what we learn to control lineage identity and tailor neuronal lineages.

Vertebrate brains are much more complex than fly brains, and there is striking developmental plasticity. It is therefore unlikely that neuronal identity is dictated by cell lineages at the single-cell level; rather, multiple similar neural stem cells produce pools of related neurons. Despite these differences, for mechanistic studies of vertebrate brain development we still need the lineage map and genetic access to specific neural progenitors.

To precisely track and manipulate distinct cells and genes, we are building CRISPR-based genetic tools that offer unlimited specificity in gene/cell targeting. We will use these tools to perform comprehensive lineage analyses followed by molecular studies to analyze lineage identity & temporal fate and elucidate cell-fating mechanisms.

In addition to development, we are also interested in investigating adult neurogenesis. Using a custom-built three-photon microscope, we will perform live cell imaging in the zebrafish model system.