John G. Flannery

112 Barker Hall
(510) 642-0178
Lab Page
AFFILIATIONS Professor of Vision Science and Optometry
Professor of Neurobiology, Department of Molecular & Cell Biology
Helen Wills Neuroscience InstituteVice Chairman, the Foundation Fighting Blindness, USAVice Chair, Fighting Blindness Ireland

Cellular and Molecular Neuroscience

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 (RPE), from environmental or poorly defined age-related factors, or the actions of other retinal neurons, glia or vascular elements. Relatively little is known about precisely why photoreceptors die in any of the many different retinal degenerations, and virtually no effective therapy exists for most of these diseases. One of the major goals of our laboratory is to develop therapeutic approaches that will slow or prevent the loss of rods, cones, RPE and other cells in retinal degenerations.

Current key questions in the laboratory are:

  1. Can a gene-based therapy be developed that would allow for the transduction of retinal cells by intravitreal injection rather than subretinal injection?
  2. Can neuroprotection occur by the targeting of a cell that spans the entire retina, the Müller cell?
  3. Can the light sensitivity of photoreceptor cells be regulated in a way to make them less sensitive to the exacerbating effects of light on opsin mutations?
  4. Can retinal ganglion cells 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 various retinal degenerations?
  5. Can gene-based delivery of a number of neuroprotective agents lead to new clinical trials for retinitis pigmentosa and other photoreceptor degenerations?

These questions will be addressed using novel genetic targeting approaches for gene delivery, the pharmacological control of ion channels to regulate PR sensitivity, the targeting of retinal ganglion cells for gene-based delivery of externally gated ion channels, and the testing of a number of neuroprotective agents in models of inherited retinal degenerations using adeno-associated virus (AAV) vectors.

The important outcomes of these studies include:

  1. the simplification of gene therapy for PR degenerations using intravitreal injection in contrast to subretinal injections (which require retinal detachment with some inherent trauma from the procedure);
  2. the potential preservation of sight through a novel approach of reducing photoreceptor sensitivity to light;
  3. the possibility of engineering retinal ganglion cells to respond to light, for use in patients who have lost all PRs from retinal degenerations;
  4. The examination of gene-based delivery of two neurotrophins that have successfully achieved neuroprotection in clinical trials of patients with Parkinson’s and Alzheimer’s disease.


Selected publications

  1.  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).
  2. 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).
  3. Flannery, J.G. & Visel, M. Adeno-associated viral vectors for gene therapy of inherited retinal degenerations. Methods in molecular biology 935, 351-369 (2013).
  4.  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).
  5. 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).
  6. 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).
  7. 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).
  8. 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). European journal of human genetics : EJHG 19, 30-35 (2011).
  9. Dalkara, D., Kolstad, K.D., Guerin, K.I., Hoffmann, N.V., Visel, M., Klimczak, R.R., Schaffer, D.V. & Flannery, J.G. AAV mediated GDNF secretion from retinal glia slows down retinal degeneration in a rat model of retinitis pigmentosa. Molecular therapy : the journal of the American Society of Gene Therapy 19, 1602-1608 (2011).
  10. Caporale, N., Kolstad, K.D., Lee, T., Tochitsky, I., Dalkara, D., Trauner, D., Kramer, R., Dan, Y., Isacoff, E.Y. & Flannery, J.G. LiGluR restores visual responses in rodent models of inherited blindness. Molecular therapy : the journal of the American Society of Gene Therapy 19, 1212-1219 (2011).
  11. 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. Investigative ophthalmology & visual science 51, 1059-1065 (2010).
  12. 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. Human gene therapy 21, 571-578 (2010).
  13. 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. The Journal of biological chemistry 284, 18980-18993 (2009).
  14. 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. Molecular vision 15, 1886-1896 (2009).
  15. 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. Molecular therapy : the journal of the American Society of Gene Therapy 17, 2088-2095 (2009).
  16. 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).
  17. 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. Molecular vision 15, 1806-1818 (2009).
  18. 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. Investigative ophthalmology & visual science 50, 5872-5879 (2009).
  19. 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. Human molecular genetics 18, 2748-2760 (2009).
  20. 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 genetics 5, e1000607 (2009).
  21. 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. Molecular therapy : the journal of the American Society of Gene Therapy 17, 2096-2102 (2009).
  22. 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. Experimental eye research 87, 197-207 (2008).
  23. Geller, S.F., Ge, P.S., Visel, M. & Flannery, J.G. In vitro analysis of promoter activity in Muller cells. Molecular vision 14, 691-705 (2008).
  24. 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. Human gene therapy 18, 871-880 (2007).
  25. Lee, E.S. & Flannery, J.G. Transport of truncated rhodopsin and its effects on rod function and degeneration. Investigative ophthalmology & visual science 48, 2868-2876 (2007).
  26. 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. Investigative ophthalmology & visual science 48, 1844-1852 (2007).
  27. Geller, S.F., Ge, P.S., Visel, M., Greenberg, K.P. & Flannery, J.G. Functional promoter testing using a modified lentiviral transfer vector. Molecular vision 13, 730-739 (2007).
  28. 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. The Journal of biological chemistry 282, 34420-34428 (2007).
  29. Lee, E.S., Burnside, B. & Flannery, J.G. Characterization of peripherin/rds and rom-1 transport in rod photoreceptors of transgenic and knockout animals. Investigative ophthalmology & visual science 47, 2150-2160 (2006).
  30. Greenberg, K.P., Lee, E.S., Schaffer, D.V. & Flannery, J.G. Gene delivery to the retina using lentiviral vectors. Advances in experimental medicine and biology 572, 255-266 (2006).
  31. Flannery, J.G. & Greenberg, K.P. Looking within for vision. Neuron 50, 1-3 (2006).
  32. 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).