Research

How do brain circuits form? What instructs self-assembly of connectivity patterns during development, and how is input from the environment used later in life? How does circuitry emerge from cell biology, and what goes wrong in mental illness and disorders of neural development? Might we be able to regenerate and correct circuitry in patients?

 

To get at these questions, our team uses a molecular systems approach to neurobiology, which includes synthetic biology, in utero electroporation, proteomics, and in vivo CRISPR genome editing to track and manipulate neural circuits and their molecules directly in the developing rodent brain. With these approaches, we can target specific circuits and molecules in vivo, introduce pathological mutations, or take control of local biochemical pathways using light, all while observing their effects on wiring patterns.

The ultimate goal of our group is to understand the in vivo mechanisms that determine circuit formation in development and circuit remodeling in adulthood; to discover how these processes deviate to alter brain circuits in neurodevelopmental disorders and mental illness; and to develop the knowhow and methodologies that may allow therapeutic intervention for the regeneration of circuits lost to disease or trauma.

Let’s get into some specifics:

Growing neuron projections forming circuitry linking the two brain hemispheres, labeled by in utero electroporation.

Circuit development

We recently developed an approach that reveals the local protein and RNA networks within axons that are in the process of forming a connection in the developing brain (Poulopoulos et al, Nature, 2019). The approach combines in utero electroporation, subcellular fractionation, and small-particle fluorescence sorting.

Subcellular RNA-Proteome Mapping of developing callosal projection neurons

Using RNA-seq and mass spectrometry, we know which molecules concentrate in axons of a particular connection, giving us a  “parts list” of the machinery that is implementing connectivity in vivo. Some of the biological processes we are currently following are cell adhesion, mTOR signaling, and local translation.

With this knowledge, we are targeting genes that produce these molecules using in vivo CRISPR genome editing to produce knockout and also knockins. This allows us to not only perform area-specific loss-of-function experiments, but also to observe and track the dynamics of these molecules under endogenous expression and sparse labeling in vivo. With some added fancy footwork in the realm of synthetic biology, we can also functionally hijack the these molecules locally using light as they go through the steps of forming or modifying brain circuitry!

Synapse development

Beyond the formation of long-range connectivity, we look up close at the critical moment when a synapse develops to complete the connection between two neurons. We have a long-term interest in the molecules that organize and coordinate the interactions across the synapse (Poulopoulos et al, Neuron, 2009; Poulopoulos et al, BiochemJ, 2012), and with our collaborators in the Blanpied lab across the street -the gurus of synapse nanostructure- we use in vivo CRISPR to tag endogenous synaptic proteins and examine their structure and function in the pre- and postsynaptic apparatuses.

 

Mental illness and disorders of neurodevelopment

We use in utero electroporation, in vivo genome editing, and 3D imaging to uncover the effects on brain circuitry of genetic variants associated with neurodevelopmental disorders and Mental illness. 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 epilepsy, autism, and schizophrenia.

Cleared mouse brain after in utero electroporation prepared for 3D imaging

For these clinically relevant projects, we work closely with collaborating labs on campus. On our epilepsy projects we work with the labs of Scott Thompson from the department of Physiology, and Peter Crino from the department of Neurology to create a full workflow from molecular, cellular, and electrophysiological endophenotyping, to EEG and behavioral monitoring in order to analyze clinically relevant mutations in mice .

On Schizophrenia,  we collaborate with the groups of Elliot Hong in Psychiatry and Seth Ament in the Institute for Genome Sciences, who provide invaluable human brain imaging and genome data from cohorts of patients, which we get to test in the mouse cerebral cortex. On neurodevelopmental disorders we collaborate with the groups of Saima Riazuddin and Zubair Ahmed who have used human genetics of isolated populations to discovered a host of new recessive gene mutations leading to sever disorders of brain development, which we can examine molecularly in the embryonic mouse brain.

To go beyond descriptions of circuit aberrations, we have developed ESI, the Endophenotype Severity Index, a ratiometric value that allows generalizable quantification and  modeling of circuit alterations associated with disease. With an interest in the circuitry of the cerebral cortex, with ESI we hope to document specific circuit and network defects in mouse models of mental illness, such as schizophrenia. Working together with our neighbors and collaborators in the Mathur lab,  we can examine both connectivity and function when looking at what circuit defects underly mental illness.

Electroporated neurons in the mouse cerebral cortex.

 

Tinkering with Cas9 (in vivo)

We are in constant need of better tools. For instance, we would like a better way to edit the genome directly in relevant cells in vivo, both for experimental purposes, and for future therapeutics. We’ve been tinkering with Cas9, using variants, mutants, and chimeras, as well as new delivery methods in vivo. All this so we can develop a way of manipulating the genome of desired cells with specificity, with minimal off target effects or adverse reactions, and with a high yield. We’ll keep you posted…

 

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.