How does the brain form? What drives self assembly, and how is input from the environment used? How do neural circuits emerge from cell biology, and what mechanisms keep connectivity changes meaningful? To get at these questions, our team uses CRISPR genome engineering together with synthetic biology in order to visualize and control subcellular pathways while brain circuits are forming and as they change with experience.



Our research aims at understanding how neurons form connections in the brain to create circuitry that serves sensation, cognition, and behavior. The phenomena underlying circuit formation straddle multiple levels of magnitude and time, giving rise to “complexes” and “dynamics”. These different levels are hierarchically bound together through a series of emergent properties that arise from interacting molecules, subcellular structures, cells, and circuits, to ultimately produce the brain and its functionalities. Our experiments examine how these different levels relate to each other, how they drive circuit formation, how they change during life-long learning, and how they are perturbed in psychiatric conditions.

We are just getting started, so more experimental details are to come! For now, here are some snippets with pretty pictures…

Cleared mouse brain after in utero electroporation. Notice the green speckles on the top hemisphere? Those are GFP electroporated neurons targeted for CRISPR genome editing!


Identifying brain circuit changes in psychiatric conditions

We use in utero electroporation, genome editing, and 3D imaging to uncover the effects on brain circuitry of genetic variants associated with neurodevelopmental and psychiatric conditions. By introducing these variants using CRISPR in select circuits of the rodent brain, we aim to identify how these connections are altered to discover circuit underpinnings of conditions such as autism, schizophrenia, and depression.

Electroporated neurons in the mouse cerebral cortex.


The cell biology behind brain circuit development

We recently developed an approach that reveals the subcellular molecular networks within axons of specific connections in the brain. We used this approach, termed Growth Cone Sorting and Subcellular RNA-Proteome Mapping (Poulopoulos, Murphy, Macklis et al, submitted), to reveal the sub-proteome of growing axons in the process of forming connections between the two hemispheres of the brain. Some of the biological processes we are currently following are cell adhesion, local translation, and synaptogenesis. Through acute in vivo genome editing using CRISPR in these neurons, we can track the dynamic behavior of select proteins within growing axons as they go through the steps of forming or modifying brain circuitry.

Molecular networks of the growth cone sub-proteome.

Hodaptics: cell-cell interactions in intact systems

The biology of cell-cell interactions is a beautifully complex and critical part of the development and function of multicellular systems. In the nervous system, this biology manifests in its extreme, with a given neuron directly contacting a bewildering and perpetually-changing number of direct cellular neighbors at any given time. It is this multitude and dynamics of cell-cell interactions that give nervous tissue its unique functionalities. However, the biology of cell-cell interactions is particularly difficult to study, as it requires experimenting on intact systems, while being able to detect and influence elusive transient interactions. To allow experimentation into this interesting biology, we have developed and are currently optimizing a new genetic technology, termed “hodaptics” (from Greek hodos- road, and haptein -to touch), that will allow us to detect and manipulate transient cell-cell interactions as they occur within intact systems such as the developing and learning brain, as well as other complex multicellular systems.