AAV Vector Engineering

We are developing custom recombinant adeno-associated viruses (AAVs) for more efficient and targeted gene transfer in vivo.

M-CREATE - for isolating novel AAV variants from large viral libraries

Ravindra Kumar, et al., Nature Methods 2020 [Github ]

AAV-PHP Production - for individual virus preparations

Challis et al., Nature Protocols 2019 [ Protocols.io link ]

AAV Production & Administration Worksheets - for individual virus preparations

Transfection Calculator

Titration Calculator

Viral Injection Volume Calculator

  • The CLOVER Center is equipped with a BSL-2 virus production facility as well as wet labs for molecular cloning, tissue processing, and macromolecular staining procedures.

  • CLOVER offers collaborative custom vector development.
  • One-on-one consultations and training for viral vector production to jump start research projects

  • Focused workshops for researchers with various backgrounds and experience levels

  • Yearly 5-day course on systemic AAVs and CLARITY as part of the NeuroNex MINT Technology Hub

Tropism is a synergy of capsid, genome, and route of administration

Multiplexed Cre-recombination-based AAV-targeted evolution

Systemic administration & tailored tropism

Space constraints necessitate clever design

Vector-assisted spectral tracing (VAST): bright labeling & tunable sparcity

Engineered opsins to pair with systemic AAV administration


Systemic AAVs in action

AAV Publications

  • Positron emission tomography imaging of novel AAV capsids maps rapid brain accumulation. Seo, J. W., Ingham, E. S., Mahakian, L., Tumbale, S., Wu, B., Aghevlian, S., Shams, S., Baikoghli, M., Jain, P., Ding, X., Goeden, N., Dobreva, T., Flytzanis, N. C., Chavez, M., Singhal, K., Leib, R., James, M. L., Segal, D. J., Cheng, R. H., Silva, E. A., Gradinaru, V., Ferrara, K. W. Nature Communications, 2020; doi: 10.1038/s41467-020-15818-4.  [ Article ]

  • Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. 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. Nature Methods, 2020; doi: 10.1038/s41592-020-0799-7.  [ Article | Cover | Caltech News Release ]

  • LRP1 is a master regulator of tau uptake and spread. Rauch, J. N., Luna, G., Guzman, E., Audouard, M., Challis, C., Sibih, Y., Leshuk, C., Hernandez, I., Wegmann, S., Hyman, B. T., Gradinaru, V., Kampmann, M., Kosik, K. S. Nature, 2020; doi: 10.1038/s41586-020-2156-5.  [ Article ]

  • Gut-seeded α-Synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice. Challis, C., Hori, A., Sampson, T. R., Yoo, B. B., Challis, R. C., Hamilton, A. M., Mazmanian, S. K., Volpicelli-Daley, L. A., Gradinaru, V. Nature Neuroscience, 2020; doi: 10.1038/s41593-020-0589-7.  [ Article | Open access link | Caltech News Release ]

  • Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics. Bedbrook, C. N., Yang, K. K., Robinson, J. E., Mackey, E. D., Gradinaru, V., & Arnold, F. H. Nature Methods, 2019; doi: 10.1038/s41592-019-0583-8.  [ Article | Open access link | Caltech News Release ]

  • Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1. Robinson, J. E., Coughlin, G. M., Hori, A. M., Cho, J. R., Mackey, E. D., Turan, Z., Patriarchi, T., Tian, L., Gradinaru, V. eLife, 2019; doi: 10.7554/eLife.48983.  [ Article ]

  • Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies. Rajendran, P. S., Challis, R. C., Fowlkes, C. C., Hanna, P., Tompkins, J. D., Jordan, M. C., Hiyari, S., Gabris-Weber, B. A., Greenbaum, A., Chan, K. Y., Deverman, B. E., Münzberg, H., Ardell, J. L., Salama, G., Gradinaru, V., Shivkumar, K. Nature Communications, 2019; doi: 10.1038/s41467-019-09770-1.  [ Article ]

  • TRIM9-Mediated Resolution of Neuroinflammation Confers Neuroprotection upon Ischemic Stroke in Mice. Zeng, J., Wang, Y., Luo, Z., Chang, L.-C., Yoo, J. S., Yan, H., Choi, Y., Xie, X., Deverman, B. E., Gradinaru, V., Gupton, S. L., Zlokovic, B. V., Zhao, Z., Jung, J. U. Cell Reports, 2019; doi: 10.1016/j.celrep.2018.12.055.  [ Article ]

  • Epigenetic landscape and AAV targeting of human neocortical cell classes. Mich, J., Hess, E., Graybuck, L., Somasundaram, S., Miller, J., Ding, Y., Shapovalova, N., Fong, O., Yao, S., Mortrud, M., Chong, P., Bertagnolli, D., Goldy, J., Casper, T., Kroll, M., Hodge, R., Bakken, T., Yao, Z., Dee, N., Cetin, A., Smith, K., Gwinn, R., Cobbs, C., Ko, A., Ojemann, J., Keene, C., Silbergeld, D., Gradinaru, V., Sunkin, S., Zeng, H., Lein, E., Tasic, B., Ting, J. and Levi, B. bioRxiv, 2019; doi: 10.1101/555318.  [ Article ]

  • Systemic AAV vectors for widespread and targeted gene delivery in rodents. Challis, R. C., Kumar, S. R., Chan, K. Y., Challis, C., Beadle, K., Jang, M. J., Kim, H. M., Rajendran, P. S., Tompkins, J. D., Shivkumar, K., Deverman, B. E., Gradinaru, V. Nature Protocols, 2019; doi: 10.1038/s41596-018-0097-3. [ Article | Cover | Open access link | High resolution fluorescent images ]

  • The Neuropeptide Tac2 Controls a Distributed Brain State Induced by Chronic Social Isolation Stress Moriel Zelikowsky, May Hui, Tomomi Karigo, Andrea Choe, Bin Yang, Mario R. Blanco, Keith Beadle, Viviana Gradinaru, Benjamin E. Deverman and David J. Anderson. Cell 2018 May 17; doi: 10.1016/j.cell.2018.03.037.  [ Article | Open access link | Caltech News Release ]

  • Viral Strategies for Targeting the Central and Peripheral Nervous Systems Bedbrook CN, Deverman BE, Gradinaru V. . Annu Rev Neurosci. 2018 Apr 25. doi: 10.1146/annurev-neuro-080317-062048.  [ Article ]

  • Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Chan, K.Y., Jang, M.J., Yoo, B.B., Greenbaum, A., Ravi, N., Wu., W.L., Sanchez-Guardado, L., Lois, C., Mazmanian, S.K., Deverman, B.E., Gradinaru, V. Nature Neuroscience, 2017; doi:10.1038/nn.4593.  [ Article | Caltech News Release | News and Views | Cover | Open access link ]

  • Global representations of goal-directed behavior in distinct cell types of mouse neocortex. Allen, W.E., Kauvar, I.V., Chen, M.Z., Richman, E.B., Yang, S.J., Chan, K., Gradinaru, V., Deverman, B.E., Luo, L., Deisseroth, K. Neuron, 2017;94, 891-907.  [ Article | DARPA Highlight ]

  • Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Deverman, B.E.*; Pravdo, P.L.; Simpson, B.P.; Kumar, S.R.; Chan, K.Y.; Banerjee, A.; Wu, W.L.; Yang, B.; Huber, N.; Pasca, S.P.; Gradinaru, V.*, Nat Biotech, 2016; doi:10.1038/nbt.3440.  [ Article | Caltech News Release | Video | CIRM Blog | F1000 Exceptional]

43 Publications by other groups using our systemic AAV viruses in FY2019 – 5 highlighted

  • Structure and flexibility in cortical representations of odour space. S.L. Pashkovski, G. Iurilli, D. Brann, D. Chicharro, K. Drummey, K. Franks, S. Panzeri, S. Robert Datta Nature 2020; 10.1038/s41586-020-2451-1

  • Glia-to-Neuron Conversion by CRISPR-CasRx Alleviates Symptoms of Neurological Disease in Mice. H. Zhao, J. Su, X. Hu, C. Zhou, H. Li, Z. Chen, Q. Xiao, B. Wang, W. Wu, Y. Sun, Y. Zhou, C. Tang, F. Liu, L. Wang, C. Feng, M. Liu, S. Li, Y. Zhang, H. Xu, H. Yao, L. Shi, H. Yang Cell 2020; 10.1016/j.cell.2020.03.024.

  • Profilin 1 delivery tunes cytoskeletal dynamics toward CNS axon regeneration. R. Pinto-Costa, S.C. Sousa, S.C. Leite, J. Nogueira-Rodrigues, T. Ferreira da Silva, D. Machado, J. Marques, A. Catarina Costa, M.A. Liz, F. Bartolini, P. Brites, M. Costell, R. Fassler, M.M. Sousa J Clinical Investigation 2020; 10.1172/JCI125771.

  • Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. J.M. Levy, W. Yeh, N. Pendse, J.R. Davis, E. Hennessey, R. Butcher, L.W. Koblan, J. Comander, Q. Liu, D.R. Liu Nature Biomedical Engineering 2020; 10.1038/s41551-019-0501-5.

  • Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain. J. Winnubst, E. Bas, T.A. Ferreira, Z. Wu, M.N. Economo, P. Edson, B.J. Arthur, C. Bruns, K. Rokicki, D. Schauder, D.J. Olbris, S.D. Murphy, D.G. Ackerman, C. Arshadi, P. Baldwin, R. Blake, A. Elsayed, M. Hasan, D. Ramirez, B. Dos Santos, M. Weldon, A. Zafar, J.T. Dudman, C.R. Gerfen, A.W. Hantman, W. Korff, S.M. Sternson, N. Spruston, K. Svoboda, J. Chandrashekar Cell 2019; 10.1016/j.cell.2019.07.042.

15 Publications by other groups using our systemic AAV viruses in FY2018 – 5 highlighted

  • Widespread transduction of astrocytes and neurons in the mouse central nervous system after systemic delivery of a self-complementary AAV-PHP.B vector. Rincon, M. Y., de Vin, F., Duque, S. I., Fripont, S., Castaldo, S. A., Bouhuijzen-Wenger, J., Holt, M. G. Gene Therapy, 2018; 10.1038/s41434-018-0005-z

  • Gene transfer with AAV9-PHP.B rescues hearing in a mouse model of Usher Syndrome 3A and transduces hair cells in a non-human primate. Gyorgy, B., Meijer, E. J., Ivanchenko, M. V., Tenneson, K., Emon, F., Hanlon, K. S., Indzhykulian, A. A., Volak, A., Karavitaki, K. D., Tamvakologos, P. I, Vezina, M., Merezovskii, V. K., Born, R. T., O'Brien, M., Lafond, J. F., Arsenijevic, Y., Kenna, M. A., Maguire, C. A., Corey, D. P. Molecular Therapy. Methods & Clinical Development, 2018; 10.1016/j.omtm.2018.11.003

  • Intravenous injection of an AAV-PHP.B vector encoding human acid a-Glucosidase rescues both muscle and CNS defects in murine Pompe Disease. Lim, J. A., yi, H., Gao, F., Raven, N., Kishnani, P. S., Sun, B. Molecular Therapy. Methods & Clinical Development, 2019; 10.1016/j.omtm.2019.01.006

  • The GPI-linked protein LY6A drives AAV-PHP.B transport across the blood-brain barrier. Hordeaux, J., Yuan, Y., Clark, P. M., Wang, Q., Martino, R. A., Sims, J. J., Bell, P., Raymond, A., Stanford, W. L., Wilson, J. M. Molecular Therapy, 2019; 10.1016/j/ymthe.2019.02.013

  • Targeted transgene activation in the brain tissue by systemic delivery of engineered AAV1 expressing CRISPRa. Lau, C. H., Ho, J. W., Lo, P. K., Tin, C. Molecular Therapy. Nucleic Acids, 2019; 10.1016/j/omtn.2019.04.015