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John G. Flannery, PhD

John Flannery.

Professor of Optometry and Vision Science

School of Optometry

Research Area
Neuroscience & Neurobiology; Molecular & Cell Biology

112 Barker Hall
Berkeley, CA . 94720


(510) 642-0178



Professor of Neurobiology, Dept. Molecular & Cell Biology
Assoc. Director, Helen Wills Neuroscience Institute


Vision Science 206D. Neuroanatomy and Neurophysiology of the Eye and Visual System


Structure and function of the neurosensory retina, photoreceptors, RPE including blood supply. Current concepts of etiology and management of major retinal conditions. Overview of diagnostic techniques in retinal imaging, electrophysiologic testing and new genetic approaches. Structure and function of the early visual pathway including retinal ganglion cells, optic nerves, lateral geniculate nucleus and visual cortex. Pupillary responses. Specialization in the visual cortex.

Research Interests

Over 100,000 Americans of all ages suffer from inherited retinal diseases, which cause a progressive loss of vision. In most IRDs, disease begins in the rods, causing vision loss from the periphery to the center, leaving patients unable to navigate their surroundings. Retinal degeneration and blindness result from the loss of rod and cone photoreceptors due to mutations in these cells or in their closely interacting and supportive retinal pigment epithelium, from environmental or poorly defined age-related factors, or the actions of other retinal neurons, glia or vascular elements. Relatively little is known about why photoreceptors die in any of the many retinal degenerations, and very little effective therapy exists for most of these diseases. One of the major goals of our laboratory is to develop therapeutic approaches that will restore vision in retinal degenerative diseases.

Gene therapy has vast potential for treating and potentially curing a number of retinal diseases, including inherited retinal degenerative diseases, glaucoma, and age-related macular degeneration. However, gene delivery technologies require significant improvements in cellular targeting, efficiency, and safety before promising findings in animal studies are translated to the clinic. The lab uses mouse models of inherited retinal degenerations to optimize transduction and gene delivery of specific retinal cell types.

Can the inner retina be manipulated in a way to add a light-receptive function, and thereby serve to transduce light in retinas that have lost their photoreceptors due to retinal degeneration? In collaboration with Co-PI Isacoff, we use mammalian cone opsins to target the surviving inner retina, specifically ganglion cells, restoring vision in mouse models of inherited retinal diseases. This compensates for their loss of input from photoreceptors, restoring light responsiveness to the retina and sending information to the brain to restore vision. In most cases, this approach is independent of the mutation that caused the photoreceptor degeneration. Exceptions to this approach may be diseases that cause RPE cell death, such as choroideremia. We employ sophisticated behavioral analysis to test not only the restoration of the ability to tell light from dark or flashing from steady light, but to determine if the animal is able to see images. Success of this program represents a major step in the creation of a retinal prosthetic based on gene therapy.

Selected Publications

Pernet, V., Joly, S., Jordi, N., Dalkara, D., Guzik-Kornacka, A., Flannery, J.G. & Schwab, M.E. Misguidance and modulation of axonal regeneration by Stat3 and Rho/ROCK signaling in the transparent optic nerve. Cell death & disease 4, e734 (2013).

Pernet, V., Joly, S., Dalkara, D., Jordi, N., Schwarz, O., Christ, F., Schaffer, D.V., Flannery, J.G. & Schwab, M.E. Long-distance axonal regeneration induced by CNTF gene transfer is impaired by axonal misguidance in the injured adult optic nerve. Neurobiology of disease 51, 202-213 (2013).

Flannery, J.G. & Visel, M. Adeno-associated viral vectors for gene therapy of inherited retinal degenerations. Methods in molecular biology 935, 351-369 (2013).

Dalkara, D., Byrne, L.C., Klimczak, R.R., Visel, M., Yin, L., Merigan, W.H., Flannery, J.G. & Schaffer, D.V. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Science translational medicine 5, 189ra176 (2013).

Pernet, V., Joly, S., Dalkara, D., Schwarz, O., Christ, F., Schaffer, D., Flannery, J.G. & Schwab, M.E. Neuronal Nogo-A upregulation does not contribute to ER stress-associated apoptosis but participates in the regenerative response in the axotomized adult retina. Cell death and differentiation 19, 1096-1108 (2012).

Lee, S.H., Kwan, A.C., Zhang, S., Phoumthipphavong, V., Flannery, J.G., Masmanidis, S.C., Taniguchi, H., Huang, Z.J., Zhang, F., Boyden, E.S., Deisseroth, K. & Dan, Y. Activation of specific interneurons improves V1 feature selectivity and visual perception. Nature 488, 379-383 (2012).

Dalkara, D., Byrne, L.C., Lee, T., Hoffmann, N.V., Schaffer, D.V. & Flannery, J.G. Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9. Gene therapy 19, 176-181 (2012)

Caporale N, Kolstad KD, Lee T, Tochitsky I, Dalkara D, Trauner D et al. LiGluR Restores Visual Responses in Rodent Models of Inherited Blindness. Mol Ther 2011; 19(7): 1212-9.

Dalkara D, Kolstad KD, Guerin KI, Hoffmann NV, Visel M, Klimczak RR et al. AAV Mediated GDNF Secretion From Retinal Glia Slows Down Retinal Degeneration in a Rat Model of Retinitis Pigmentosa. Mol Ther 2011.

Vastinsalo, H., Jalkanen, R., Dinculescu, A., Isosomppi, J., Geller, S., Flannery, J.G., Hauswirth, W.W. & Sankila, E.M. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). Eur J Hum Genet 19, 30-35 (2011).

Kolstad, K.D., Dalkara, D., Guerin, K., Visel, M., Hoffmann, N., Schaffer, D.V. & Flannery, J.G. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration. Hum Gene Ther 21, 571-578 (2010).

Klimczak, R.R., Koerber, J.T., Dalkara, D., Flannery, J.G. & Schaffer, D.V. A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Muller cells. PLoS One 4, e7467 (2009).

Tackenberg, M.A., Tucker, B.A., Swift, J.S., Jiang, C., Redenti, S., Greenberg, K.P., Flannery, J.G., Reichenbach, A. & Young, M.J. Muller cell activation, proliferation and migration following laser injury. Mol Vis 15, 1886-1896 (2009).

Isosomppi, J., Vastinsalo, H., Geller, S.F., Heon, E., Flannery, J.G. & Sankila, E.M. Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane. Mol Vis 15, 1806-1818 (2009).

Liu, H., Wang, M., Xia, C.H., Du, X., Flannery, J.G., Ridge, K.D., Beutler, B. & Gong, X. Severe retinal degeneration caused by a novel rhodopsin mutation. Invest Ophthalmol Vis Sci 51, 1059-1065 (2010).

Geller, S.F., Guerin, K.I., Visel, M., Pham, A., Lee, E.S., Dror, A.A., Avraham, K.B., Hayashi, T., Ray, C.A., Reh, T.A., Bermingham-McDonogh, O., Triffo, W.J., Bao, S., Isosomppi, J., Vastinsalo, H., Sankila, E.M. & Flannery, J.G. CLRN1 is nonessential in the mouse retina but is required for cochlear hair cell development. PLoS Genet 5, e1000607 (2009).

Dalkara, D., Kolstad, K.D., Caporale, N., Visel, M., Klimczak, R.R., Schaffer, D.V. & Flannery, J.G. Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous. Mol Ther 17, 2096-2102 (2009).

Koerber, J.T., Klimczak, R., Jang, J.H., Dalkara, D., Flannery, J.G. & Schaffer, D.V. Molecular evolution of adeno-associated virus for enhanced glial gene delivery. Mol Ther 17, 2088-2095 (2009).

Geng, Y., Greenberg, K.P., Wolfe, R., Gray, D.C., Hunter, J.J., Dubra, A., Flannery, J.G., Williams, D.R. & Porter, J. In vivo imaging of microscopic structures in the rat retina. Invest Ophthalmol Vis Sci 50, 5872-5879 (2009).

Tian, G., Zhou, Y., Hajkova, D., Miyagi, M., Dinculescu, A., Hauswirth, W.W., Palczewski, K., Geng, R., Alagramam, K.N., Isosomppi, J., Sankila, E.M., Flannery, J.G. & Imanishi, Y. Clarin-1, encoded by the Usher Syndrome III causative gene, forms a membranous microdomain: possible role of clarin-1 in organizing the actin cytoskeleton. J Biol Chem 284, 18980-18993 (2009).

Geng, R., Geller, S.F., Hayashi, T., Ray, C.A., Reh, T.A., Bermingham-McDonogh, O., Jones, S.M., Wright, C.G., Melki, S., Imanishi, Y., Palczewski, K., Alagramam, K.N. & Flannery, J.G. Usher
syndrome IIIA gene clarin-1 is essential for hair cell function and associated neural activation. Hum Mol Genet 18, 2748-2760 (2009).

Guerin, K., Gregory-Evans, C.Y., Hodges, M.D., Moosajee, M., Mackay, D.S., Gregory-Evans, K. & Flannery, J.G. Systemic aminoglycoside treatment in rodent models of retinitis pigmentosa. Exp Eye Res 87, 197-207 (2008).

Geller, S.F., Ge, P.S., Visel, M. & Flannery, J.G. In vitro analysis of promoter activity in Muller cells. Mol Vis 14, 691-705 (2008).
Paskowitz, D.M., Greenberg, K.P., Yasumura, D., Grimm, D., Yang, H., Duncan, J.L., Kay, M.A., Lavail, M.M., Flannery, J.G. & Vollrath, D. Rapid and stable knockdown of an endogenous gene in retinal pigment epithelium. Hum Gene Ther 18, 871-880 (2007).

Chen, Y., Hu, Y., Lu, K., Flannery, J.G. & Ma, J.X. Very low density lipoprotein receptor, a negative regulator of the wnt signaling pathway and choroidal neovascularization. J Biol Chem 282, 34420-34428 (2007).

Geller, S.F., Ge, P.S., Visel, M., Greenberg, K.P. & Flannery, J.G. Functional promoter testing using a modified lentiviral transfer vector. Mol Vis 13, 730-739 (2007).

Lee, E.S. & Flannery, J.G. Transport of truncated rhodopsin and its effects on rod function and degeneration. Invest Ophthalmol Vis Sci 48, 2868-2876 (2007).

Greenberg, K.P., Geller, S.F., Schaffer, D.V. & Flannery, J.G. Targeted transgene expression in muller glia of normal and diseased retinas using lentiviral vectors. Invest Ophthalmol Vis Sci 48, 1844-1852 (2007).

Greenberg, K.P., Lee, E.S., Schaffer, D.V. & Flannery, J.G. Gene delivery to the retina using lentiviral vectors. Adv Exp Med Biol 572, 255-266 (2006).

Lee, E.S., Burnside, B. & Flannery, J.G. Characterization of peripherin/rds and rom-1 transport in rod photoreceptors of transgenic and knockout animals. Invest Ophthalmol Vis Sci 47, 2150-2160 (2006).

Flannery, J.G. & Greenberg, K.P. Looking within for vision. Neuron 50, 1-3 (2006).

Hauswirth, W.W., Li, Q., Raisler, B., Timmers, A.M., Berns, K.I., Flannery, J.G., LaVail, M.M. & Lewin, A.S. Range of retinal diseases potentially treatable by AAV-vectored gene therapy. Novartis Foundation symposium 255, 179-188; discussion 188-194 (2004).