Faculty Research Page

John Flannery

John G. Flannery

Professor of Neurobiology

Lab Homepage: http://mcb.berkeley.edu/labs/flannery/

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Research Interests

Molecular Biology and Gene Therapies for Inherited Retinal Degenerations

Inherited forms of retinal degeneration, which afflict 1 in 3000 people worldwide, arise primarily from mutations in transcripts expressed in rod and cone photoreceptors and retinal pigment epithelial cells. The outer retina is therefore the primary target for ocular gene therapies. Photoreceptor degeneration is a very genetically heterogeneous disorder; with mutations in over 200 loci identified. Our laboratory focuses on understanding the  genetic and mechanistic underpinning of photoreceptor degeneration, and developing rational therapies for these blinding conditions. The genetic and biochemical diversity of photoreceptor degnereration presents major challenges for therapy as there are many pathways to cell death. 

Gene therapy has great potential for treating retinal diseases including glaucoma, age-related macular degeneration, and inherited photoreceptor diseases.   To date, most gene therapies have targeted monogenic recessive retinal diseases and employed viral vectors to transfer a 'normal ' copy of the mutated gene to the affected cell. We are currently developing animal models of inherited retinal diseases to study the disease processes.  In parallel, we are designing viral mediated therapies for autosomal dominant and recessive retinal degnenerations. 

Current Projects

The retina is a complex tissue in the back of the eye that contains the rod and cone photoreceptor cells. The photoreceptors connect to a network of retinal interneurons. The adjacent retinal pigment epithelium (RPE) supports many of the retina's metabolic functions. The retina is susceptible to a number of blinding diseases, such as age-related macular degeneration, diabetic retinopathy and other inherited retinal degenerations. The inherited retinal degenerations are typified by retinitis pigmentosa (RP), which results in blindness from destruction of photoreceptor cells, and the RPE. This group of conditions affects approximately 100,000 people in the United States. To date, more than 130 genes causing inherited retinopathies in humans have been identified. This makes it possible to identify the cause of RP in approximately 50 percent of patients and the cause of Usher syndrome in 75 percent of patients.

Gene identifications in humans have allowed us to examine the biochemical pathways in these diseases. In addition, gene identification in patients permits us to identify naturally occurring animal models or create new transgenic or knockout animal models with retinal degeneration due to defects in the gene homologs. In particular, we have the examined retinal degeneration in the naturally arising rd mouse strains (defects in the b-subunit of phosphodiesterase). We have also developed transgenic rats, expressing dominant rhodopsin mutations. Most recently we have developed a knockout mouse model of Usher syndrome type 3, which caused progressive blindness and deafness in patients. These animal models are the subject of study to determine the pathophysiological mechanisms whereby these gene defects lead to photoreceptor degeneration and hopefully will lead to pilot studies of novel therapies for retinal degeneration.

Development of effective treatments for retinal diseases.

With increasing insight into the molecular etiologies of several inherited retinal and macular dystrophies, studies from ours and many laboratories have defined several promising therapeutic strategies.

Current projects in our lab involve development of retinal cell specific viral vectors based upon lentivirus and adeno-associated viruses. In previous work, we have demonstrated significant slowing of photoreceptor degeneration in several animal models following gene transfer of neurotrophic agents. Another promising strategy for dominantly inherited retinal diseases involves directly targeting the mutant mRNA product using Talens, CRISPR, and siRNA constructs. For recessive null diseases, gene replacement is an option.

We find that gene therapy has vast potential for treating and potentially curing a number of inherited photoreceptor diseases. However, gene delivery technologies require significant improvements in cellular targeting, efficiency, and safety before promising findings in animal studies are translated to the clinic. In particular, for retinal gene therapy it would be highly advantageous to transduce a single cell type that spans the entire retina after an intravitreal injection of a gene delivery vehicle for the subsequent secretion of a general neuroprotective factor throughout the retina. Unfortunately, there is no vector capable of efficiently infecting the cell type that meets these needs, Muller cells. Vectors based on adeno-associated virus (AAV) have proven themselves to be highly promising in numerous retinal disease models, but they are also incapable of Muller cell infection. Recently, we have developed novel lentiviral vectors with new properties, including altered receptor binding, which are capable of efficient Muller cell transduction. In parallel, the basic mechanisms of AAV transduction of Muller cells will be explored in order to develop new AAV pseudotypes capable of Muller cell transduction. The novel approaches developed in this work will have general impact for the molecular engineering of enhanced viral gene delivery vehicles, and future work will focus on testing these vectors in an animal model of retinal disease.

Selected Publications

Neuron-glia signaling in developing retina mediated by neurotransmitter spillover.Rosa JM, Bos R, Sack GS, Fortuny C, Agarwal A, Bergles DE, Flannery JG, Feller MB. Elife. 2015 Aug 14;4. doi: 10.7554/eLife.09590.  
Optogenetic Vision Restoration Using Rhodopsin for Enhanced Sensitivity. Gaub BM, Berry MH, Holt AE, Isacoff EY, Flannery JG.Mol Ther. 2015 Jul 3. doi: 10.1038/mt.2015.121.
Gene therapy into photoreceptors and Müller glial cells restores retinal structure and function in CRB1 retinitis pigmentosa mouse models.
Pellissier LP, Quinn PM, Alves CH, Vos RM, Klooster J, Flannery JG, Heimel JA, Wijnholds J. Hum Mol Genet. 2015 Jun 1;24(11):3104-18. doi: 10.1093/hmg/ddv062. Epub 2015 Feb 20.
CRALBP supports the mammalian retinal visual cycle and cone vision. Xue Y, Shen SQ, Jui J, Rupp AC, Byrne LC, Hattar S, Flannery JG, Corbo JC, Kefalov VJ. J Clin Invest. 2015 Feb;125(2):727-38. doi: 10.1172/JCI79651. Epub 2015 Jan 20.
Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells. Gaub BM, Berry MH, Holt AE, Reiner A, Kienzler MA, Dolgova N, Nikonov S, Aguirre GD, Beltran WA, Flannery JG, Isacoff EY. Proc Natl Acad Sci U S A. 2014 Dec 8. pii: 201414162.PMID: 25489083  

Viral-mediated RdCVF and RdCVFL expression protects cone and rod photoreceptors in retinal degeneration.Byrne LC, Dalkara D, Luna G, Fisher SK, Clérin E, Sahel JA, Léveillard T, Flannery JG. J Clin Invest. 2014 Nov 21. pii: 65654. doi: 10.1172/JCI65654. PMID: 25415434  

The Expression Pattern of Systemically Injected AAV9 in the Developing Mouse Retina Is Determined by Age. Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG. Mol Ther. 2014 Sep 16. doi: 10.1038/mt.2014.181.  PMID: 25224467  

Visual stimulation switches the polarity of excitatory input to starburst amacrine cells. Vlasits AL, Bos R, Morrie RD, Fortuny C, Flannery JG, Feller MB, Rivlin-Etzion M. Neuron. 2014 Sep 3;83(5):1172-84. doi: 10.1016/j.neuron.2014.07.037. Epub 2014 Aug 21. PMID: 25155960  

Imaging light responses of foveal ganglion cells in the living macaque eye. Yin L, Masella B, Dalkara D, Zhang J, Flannery JG, Schaffer DV, Williams DR, Merigan WH. J Neurosci. 2014 May 7;34(19):6596-605. doi: 10.1523/JNEUROSCI.4438-13.2014. PMID: 24806684

Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse. Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG. Gene Ther. 2014 Jun;21(6):585-92. doi: 10.1038/gt.2014.31. Epub 2014 Apr 3. PMID: 24694538  

Advances in AAV vector development for gene therapy in the retina. Day TP, Byrne LC, Schaffer DV, Flannery JG. Adv Exp Med Biol. 2014;801:687-93. doi: 10.1007/978-1-4614-3209-8_86.  

Targeted ablation of Crb2 in photoreceptor cells induces retinitis pigmentosa. Alves CH, Pellissier LP, Vos RM, Garcia Garrido M, Sothilingam V, Seide C, Beck SC, Klooster J, Furukawa T, Flannery JG, Verhaagen J, Seeliger MW, Wijnholds J. Hum Mol Genet. 2014 Jul 1;23(13):3384-401. doi: 10.1093/hmg/ddu048. Epub 2014 Feb 2. PMID: 24493795
Vacca, O., Darche, M., Schaffer, D.V., Flannery, J.G., Sahel, J.A., Rendon, A. & Dalkara, D. AAV-mediated gene delivery in Dp71-null mouse model with compromised barriers. Glia 62, 468-476 (2014).
Alves, C.H., Pellissier, L.P., Vos, R.M., Garcia Garrido, M., Sothilingam, V., Seide, C., Beck, S.C., Klooster, J., Furukawa, T., Flannery, J.G., Verhaagen, J., Seeliger, M.W. & Wijnholds, J. Targeted ablation of Crb2 in photoreceptor cells induces retinitis pigmentosa. Human molecular genetics (2014).
Pernet V, Joly S, Dalkara D, Jordi N, Schwarz O, Christ F, Schaffer DV, Flannery JG, Schwab ME. Long-distance axonal regeneration induced by CNTF gene transfer is impaired by axonal misguidance in the injured adult optic nerve. Neurobiol Dis. 2013 Mar;51:202-13.

Pernet, V., S. Joly, D. Dalkara, O. Schwarz, F. Christ, D. Schaffer, J. G. Flannery and M. E. Schwab (2012). "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 Differ 19(7): 1096-1108.

Dalkara, D., L. C. Byrne, T. Lee, N. V. Hoffmann, D. V. Schaffer and J. G. Flannery (2012). "Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9." Gene Ther19(2): 176-181.

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 JG et al. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). Eur J Hum Genet 2011; 19(1): 30-5.

Kolstad KD, Dalkara D, Guerin K, Visel M, Hoffmann N, Schaffer DV et al. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration. Hum Gene Ther 2010; 21(5): 571-8.

Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer DV. A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Muller cells.PLoS One 2009; 4(10): e7467.

Tackenberg MA, Tucker BA, Swift JS, Jiang C, Redenti S, Greenberg KP et al. Muller cell activation, proliferation and migration following laser injury. Mol Vis 2009; 15: 1886-96.

Isosomppi J, Vastinsalo H, Geller SF, Heon E, Flannery JG, Sankila EM. Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane. Mol Vis 2009; 15: 1806-18.

Geller SF, Guerin KI, Visel M, Pham A, Lee ES, Dror AA et al. CLRN1 is nonessential in the mouse retina but is required for cochlear hair cell development. PLoS Genet 2009; 5(8): e1000607.

Dalkara D, Kolstad KD, Caporale N, Visel M, Klimczak RR, Schaffer DV et al. Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous.Mol Ther 2009; 17(12): 2096-102.

Koerber JT, Klimczak R, Jang JH, Dalkara D, Flannery JG, Schaffer DV. Molecular evolution of adeno-associated virus for enhanced glial gene delivery. Mol Ther 2009; 17(12): 2088-95.

Last Updated 2015-08-27