Genetic tools and technologies for cell type targeting and editing

A key obstacle to understanding brain circuits is the diversity of neuronal cell types. Over the past two decades, we have pioneered a genetic dissection of cortical circuits through systematic targeting of neuronal cell types in the mouse. Leveraging molecular markers and developmental programs, we use gene targeting in embryonic stem cells to generate over 60 driver and reporter mouse lines targeting major types and lineages of GABAergic inhibitory interneurons and glutamatergic excitatory projection neurons. We further design sophisticated combinatorial strategies that incorporate viral vectors to target increasingly more specific subtypes10-12. These genetic tools have transformed the study of cortical circuits by enabling experimental access and integration of a full range of modern techniques to an increasingly comprehensive set of neuron types. Since 2017, Dr. Huang has been directing a Comprehensive Center for Mouse Brain Cell Atlas as part of the US BRAIN Initiative Cell Census Network (BICCN). A major goal of our Center is to build genetic tools for projection neuron types across the cortico-striatal-thalamic system. These tools will greatly empower a large community of neuroscientists to study the cortical-striatal-thalamic system - prominent brain networks that mediate a wide range of sensory, motor, emotional, and cognitive functions.

Beyond germline genetic engineering in a few model organisms (e.g. mouse, Drosophila), advances in biomedical research require cell type technologies that are easy, facile, scalable, and generalizable across species including human. We have recently invented a new class of cell type technology that leverages cell type-defining RNAs. CellREADR, Cell access through RNA sensing by Endogenous ADAR (adenosine deaminase acting on RNA), harnesses an RNA sensing and editing mechanism ubiquitous to all animal cells for detecting the presence of specific cellular RNAs and switching on the translation of effector proteins to monitor and manipulate the cell type. Deployed as a single RNA molecule operating through Watson-Crick base pairing, CellREADR is inherently specific, easy, scalable, programmable, and general. As RNAs are the universal messengers of gene expression that underlie cell identities and states across organ systems and species, CellREADR will have a wide impact across biomedical research. We are devoting major efforts to the further innovation and optimization of CellREADR for cell type editing across organ systems and species including human tissues. With its capacity to sense and program cellular physiology, we will harness CellREADR for cell type precision diagnostics and therapeutics.

Related Publications

Huang ZJ (2014) Toward a genetic dissection of cortical circuits in the mouse. Neuron. 2014 Sep 17;83(6):1284-302. doi: 10.1016/j.neuron.2014.08.041. PMID: 25233312 Free PMC article. Review.

He M, Huang ZJ (2018) Genetic approaches to access cell types in mammalian nervous systems.

Curr Opin Neurobiol. 2018 Jun;50:109-118. doi: 10.1016/j.conb.2018.02.003. Epub 2018 Feb 22. PMID: 29471215

Qian, Y, Li, J, Zhao, S, Wang, B, An, X, Huang, ZJ (2021) Cell Type Access by Programmable RNA sensing. Submitted.

Matho, K.S., Huilgol, D., Galbavy, W., Kim, G., He, M., An, X., Lu, J., Wu, P., Di Bella, D., Shetty, A, Palaniswamy, R., Hatfield, J., Raudales, R., Narasimhan, A., Gamache, E., Levine, J., Tucciarone, J., Mitra, M., Osten, P., Arlotta, P., Huang, Z.J. Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex. Nature. 2021 Oct;598(7879):182-187. doi: 10.1038/s41586-021-03955-9. Epub 2021 Oct 6. PMID: 34616069

He M, Tucciarone J, Lee S, Nigro MJ, Kim Y, Levine JM, Kelly SM, Krugikov I, Wu P, Chen Y, Gong L, Hou Y, Osten P, Rudy B, Huang ZJ. Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex. Neuron. 2016 Sep 21;91(6):1228-43.  PMCID: PMC5223593

He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron. 2012 Jan 12;73(1):35-48. PMCID: PMC3270494.

Taniguchi H, He M, Wu P, Kim S, Paik R, Sugino K, Kvitsiani D, Fu Y, Lu J, Lin Y, Miyoshi G, Shima Y, Fishell G, Nelson SB, Huang ZJ. A resource of Cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex. Neuron. 2011 Sep 22;71(6):995-1013. PMCID: PMC3779648.

Funding support

BRAIN Initiative U19; A Comprehensive Center for Mouse Brain Cell Atlas

NIMH BRAIN Initiative RF1; Large scale discovery and validation of brain cell enhancers for viral targeting and circuit manipulation

NIH Director’s Pioneer Award; RNA-programmable cell type editing and therapy


Derek Southwell, Duke University Department of Neurosurgery

Jesse Gillis, University of Toronto/Cold Spring Harbor Laboratory