Engineering viruses to deliver gene therapy to targeted cell populations
Adeno-associated viruses are used to deliver gene therapy for genetic diseases, but they often have trouble reaching certain parts of the body; we work on methods for engineering the virus protein shell to reach hard-to-reach cell types, like neurons in the brain, and for better understanding where and how these viruses operate.
Viruses can be humanity's Trojan horses when it comes to reaching hard to get places in the body and delivering a therapeutic, like gene therapy. In our case, we are interested in different neuronal populations in the brain. We work with colleagues in Viviana Gradinaru's group at Caltech to process and analyze sequencing data recovered from mouse brain tissue samples that have been injected with custom engineered adeno-associated viruses. We are investigating what components of the virus capsid contribute to making it past the blood-brain barrier and into specific types of cells, and seeking to better to understand their functional fingerprint. Some elements of our work include:
Analyzing next-generation sequencing datasets to quantify relative transduction efficiency of large libraries of viral variants
Performing machine learning classification and regression of libraries of viral variants to find patterns in enrichment and cell-type specificity and make predictions on new variants
Using unsupervised clustering methods to find classes of viral variants with similar properties
Developing single-cell sequencing methodologies to understand, at a deeper level, the behavior of these viruses
Brown, D., Altermatt, M., Dobreva, T., Park, J. H., Kumar, S. R., Chen, X., Coughlin, G. M., Pool, A., Thomson, M., Gradinaru, V. A Computational and Experimental Platform for Detecting Full Transcriptome Cell Type Tropism of Lowly Expressed Barcoded and Pooled AAV Variants via Single-Cell RNA Sequencing. 2020 ASGCT Annual Meeting Abstracts. (2020). Molecular Therapy, 28(4), 1–592. https://doi.org/10.1016/j.ymthe.2020.04.019
Seo, J.W., Ingham, E.S., Mahakian, L. et al. Positron emission tomography imaging of novel AAV capsids maps rapid brain accumulation. Nat Commun 11, 2102 (2020)
Ravindra Kumar, S., Miles, T. F., Chen, X., Brown, D., Dobreva, T., Huang, Q., Ding, X., Luo, Y., Einarsson, P. H., Greenbaum, A., Jang, M. J., Deverman, B. E., & Gradinaru, V. (2020). Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. Nature Methods. https://doi.org/10.1038/s41592-020-0799-7
S. Kumar, X. Chen, B. E. Deverman, D. Brown, T. Dobreva, Q. Huang, X. Ding, Y. Luo, P. H. Einarsson, N. Goeden, N. Flytzanis, A. Greenbaum, V. Gradinaru. Multiplexed-CREATE Selection Yields AAV Vectors Targeting Different Cell Types of the Central Nervous System Following Systemic Delivery. Abstract No. 99. Washington, D.C.: ASGCT, 2019. Online.
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T. Dobreva, D. Brown, S. Kumar, Y. Luo, R. Hurt, B. E. Deverman, V. Gradinaru. "Engineering novel adeno-associated viruses for enhanced transduction and target specificity across the CNS by adopting high-throughput in vivo and in silico methods". Session No. 468. Neuroscience 2016 Abstracts. San Diego, CA: Society for Neuroscience, 2016. Online.
High-Throughput Method Speeds Discovery of Improved Vectors For Gene Delivery To Diverse Brain Cell Types
Using deep sequencing to guide evolution of AAVs has yielded rich datasets, and new viral variants, such as one that is better able to transduce brain vasculature