2026 Theses Doctoral

On-demand Phototagging for Molecular Analyses of Functionally Identified Pyramidal Neurons in Hippocampal CA1

Shi, Jingcheng

A long standing and unresolved challenge in neuroscience is how to relate the activity of a single neuron in the context of circuit and behavior to the molecular identity of the same neuron. Neurons are the building blocks of the nervous system, while the molecular identities influence the function of individual neurons. Although the diverse profiles of molecular and functional identities of neurons have been thoroughly probed individually, discovering the link between these two fundamental properties have been slow due to limitations of tools.

This thesis details, in one part, the method development to introduce a new complementary method for correlated analysis of functional and molecular identities, and the other part to use this method to investigate the molecular identities of functionally identified pyramidal neurons in hippocampal CA1 and how the results from such work generate new testable hypotheses related to memory formation and stabilization.

In the included works, in Chapter 2, I demonstrate 2P-NucTag, an in vivo framework for physiological recording of neuronal activities followed by on-demand phototagging to label functionally identified neuronal nuclei, and validation work to show how it works with post hoc methods for molecular identification and characterization with existing methodologies. I show how 2P-NucTag can be utilized to study the molecular profiles of the hippocampal pyramidal cell population that only differ in their activity patterns.

I resolved the molecular differences between ‘place’ and ‘silent’ cells, and the more granular difference between ‘day 0’ place cells and ‘recurring’ place cells as the spatial coding of these neurons stabilizes over days when the animal explores the same environment. I found that 2P-NucTag can work as a complementary method for on-demand in vivo phototagging for downstream molecular analyses, and that despite activity as the only differences between these cell types probed in vivo, their molecular differences can be resolved by 2P-NucTag and validated using existing approaches. My results provided a new platform for correlated analyses across neuroscience sub-disciplines and generated new hypotheses that challenge the prevailing understanding that pyramidal cells in the neocortex are largely homogeneous.