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Publications of the Week

Enhancer Viruses for Combinatorial Cell-Subclass-Specific Labeling

By May 20, 2021May 21st, 2021No Comments

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This week, we profile a recent publication in Neuron
from Dr. Tanya Daigle (pictured) at Allen Institute for Brain Science.

Can you provide a brief overview of your lab’s current research focus?
My team is developing adeno-associated viruses (AAVs) and transgenic tools to target and perturb a diverse array of brain cell types in mouse and beyond.  We leverage single cell epigenomics and transcriptomic data to identify marker genes and regulatory elements that label discrete neuronal populations and utilize an array of molecular approaches to create new genetic tools. We characterize the tools by evaluating reporter expression patterns in the brain and by measuring the physiological response properties of the targeted cell types. We determine how to best utilize the tools in combination with one another and ultimately provide genetic recipes for targeting brain cell types to the neuroscience community. Finally, through cross-team work, we also test and validate the tools in multiple mammalian species, including non-human primate and human, with the end goal of creating an arsenal of genetic tools for both basic and translational applications.

What is the significance of the findings in this publication?
For decades neuroscientists have been limited to only a handful of promoters or regulatory elements that drive cell type-specific gene expression in the mammalian brain. This has resulted in a heavy reliance on transgenic mouse lines, which take a long time to generate, are expensive to maintain, and are limited to the engineered species. In our publication and the associated paper in Cell Reports, we describe the creation and characterization of a collection of AAVs to target diverse brain cell types.  We show that these tools can be combined with one another and existing transgenics to do experiments previously impossible with existing genetic approaches. Additionally, we show AAVs initially intended only for use in mouse can also be used in human ex vivo brain slices to label the homologous cell type. This approach gives unprecedented flexibility to explorations of cell types and may enable the development of gene-based therapeutics for pervasive and debilitating brain disorders.

What are the next steps for this research?
The two publications are proof-of-concept that we can identify cell type-specific regulatory elements and create AAVs to target a small handful of cell types in the brain of multiple species. We know from large-scale transcriptomic analyses of single cells that a large diversity of types exists in the brain and for many, there are no existing genetic tools that can be used for targeting. Therefore, we plan to expand our scope of work in this space and develop a comprehensive suite of AAVs for many diverse cell types across many different brain regions. We will also develop strategies to refine viral labeling patterns in the brain and develop viruses for functional experiments.

This work was funded by:
We wish to thank the Allen Institute founder, Paul G. Allen, for his vision, encouragement, and support. This work was funded by the Allen Institute for Brain Science and by US National Institutes of Health (NIH) awards R01DA036909 from the National Institute on Drug Abuse; RF1MH121274 from the BRAIN Initiative award; and RF1MH114126 from the National Institute of Mental Health.

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