About

Professor John G. Flannery leads the Flannery Lab, which is dedicated to advancing preclinical gene therapy and vision restoration. The lab's primary research focus is on optimizing therapeutic strategies that utilize adeno-associated viruses to deliver gene replacements. These approaches are applied to models of inherited retinal degenerative diseases, aiming to develop effective treatments for these conditions. The Flannery Lab's work represents a significant effort in the field of gene therapy, particularly in the context of vision science and retinal disease research.

Research topics

• Biology
• Genetics
• Medicine
• Computer Science
• Bioinformatics
• Neuroscience
• Computational biology
• Ophthalmology
• Immunology
• Virology
• Evolutionary biology
• Pathology
• Optometry

Selected publications

• Optogenetic restoration of high-sensitivity vision using ChRmine- and ChroME-based channelrhodopsins

  Scientific Reports · 2025-07-01 · 5 citations

  articleOpen accessSenior author

  Optogenetic gene therapy is a promising mutation-independent treatment that aims to restore visual perception in patients blinded by retinal diseases that cause photoreceptor degeneration. Still, low sensitivity or slow kinetics of currently utilized optogenetic proteins limit the efficacy of such approaches. Here, we evaluated the therapeutic potential of three channelrhodopsin variants: ChRmine, from the algae Rhodomonas lens, ChRmine-T119A, a faster-closing ChRmine variant, and ChroME2s, a second-generation Chronos-based opsin.We expressed these opsins in retinal ganglion cells of rd1 mice, a model of severe retinal degeneration. Single cell electrophysiology demonstrates opsin's large sensitivity to a range of light intensities as well as opsin-expressing retinal ganglion cells generated action potentials in response to light stimulation. Behavioral tests showed ChRmine-T119A's efficacy at 360 lux compared to unmodified ChRmine and ChroME2s. ChRmine and ChroME2s did restore light perception at higher light intensities. Additionally, our dose-response study with ChRmine-T119A revealed that lower viral titers were more effective at restoring light sensitivity. Our study demonstrates that these ChRmine- and ChroME-based opsins can enhance vision in late-stage blinding diseases.

  PublisherOA PDFDOI

• Truncated complement factor H Y402 gene therapy rescues C3 glomerulonephritis

  Molecular Therapy · 2025-04-24 · 1 citations

  articleOpen access

  mouse model of C3G. We tested three different tCFH vectors and found significant differences in their relative transduction efficiency and therapeutic efficacy. These discoveries motivate the development of AAV-mediated tCFH replacement therapy for patients with C3G while simultaneously demonstrating proof of concept for AAV-mediated tCFH gene augmentation therapy for patients with AMD.

  PublisherDOI

• Dissecting the biological complexity of age-related macular degeneration: Is it one disease, multiple separate diseases, or a spectrum?

  Experimental Eye Research · 2025-02-19 · 4 citations

  reviewOpen access

  Clinicians recognize the heterogeneity of age-related macular degeneration (AMD) in presentation, progression, and treatment response, as well as the challenges in distinguishing it from other macular degenerations. As part of the 2024 Ryan Initiative for Macular Research meeting, a group of clinician-scientists and basic scientists were convened to consider the question of whether AMD should be classified as a single disorder or a spectrum of conditions. To answer this question, we reviewed research on several “dimensions” that constitute AMD risk or pathogenesis: genetics, ancestry, retinal imaging findings, diet and environment, aging, and outer retinal molecular and cellular pathways. The group reached a consensus that AMD represents a heterogeneous collection of disease states arising from the interplay of these dimensions. This heterogeneity can be conceived of as a “cloud” of AMD phenotypes. Defining subtypes within this “cloud” requires longitudinal cohorts of well-genotyped and phenotyped patients who progress from no AMD through late AMD, analyzed by unsupervised learning. Comparing the AMD subtypes that emerge from this analysis, especially -omics data from each subtype, will illuminate biology that is applicable to certain subtypes of AMD patients and molecular pathogenic mechanisms that universally apply to all AMD. This knowledge will, in turn, drive improved drug development. • Rather than being a single disease, AMD is either a continuous or discontinuous spectrum with varying presentations, progression rates, outcomes, and responses to treatment. • Multiple factors contribute to AMD, including genetics, ancestry, retinal imaging findings, diet/environment, aging, and outer retina biological pathways. • The factors that contribute to AMD can be conceived of as axes on a multi-dimensional coordinate system, with AMD occupying a cloud of points in this coordinate system. • Well-characterized longitudinal studies of AMD patients need to be combined with unsupervised learning to define disease subtypes that exist within the AMD “cloud”. • With AMD subtypes defined, comparing omics data between subtypes will identify biological pathways and therapeutic targets critical for specific AMD subtypes.

  PublisherDOI

• Addressing Challenges in Developing Treatments for Inherited Retinal Diseases: Recommendations From the Third Monaciano Symposium

  Translational Vision Science & Technology · 2025-08-27 · 4 citations

  reviewOpen access

  Over the past decade, efforts focused on developing genetic therapies for inherited retinal diseases have advanced steadily to clinical trials and the development of a treatment, fueling optimism for the potential of precision medicines to provide safe and effective therapies for these rare conditions. Although several ongoing programs remain poised for success, numerous challenges have negatively impacted the ability to obtain regulatory approvals. The present position paper briefly summarizes recent advances and challenges in developing therapeutics for inherited retinal diseases, and presents a set of recommendations for moving the field forward. The priorities identified are discussed in terms of progress made and future needs, focusing on areas including patient support, disease mechanisms, outcome measures, and therapy approvals. A key point is the potential value of restructuring collaborative interactions into broadly resourced enterprises that are comprehensive in scope across critical areas of science, business, and medicine.

  PublisherOA PDFDOI

• Truncated Complement Factor H Y402 Gene Therapy Cures C3 Glomerulonephritis

  bioRxiv (Cold Spring Harbor Laboratory) · 2024

  • Immunology
  • Medicine
  • Biology

  -/- mouse model of C3G. While past efforts to treat C3G using exogenous human CFH resulted in limited success before immune rejection led to a foreign protein response, our findings demonstrate the capacity for long-term AAV-mediated delivery of truncated CFH (tCFH) to restore inhibition of the alternative pathway of complement and ultimately reverse C3G without immune rejection. Comparing results from the administration of several tCFH vectors also revealed significant differences in their relative efficiency and efficacy. These discoveries pave the way for subsequent development of AAV-mediated tCFH replacement therapy for patients with C3G, while simultaneously demonstrating proof of concept for a parallel AAV-mediated tCFH gene augmentation therapy for patients with AMD.

  PublisherDOI

• Gene Therapy for Inherited Retinal Disease: Long-Term Durability of Effect

  Ophthalmic Research · 2022-09-14 · 69 citations

  reviewOpen access

  The recent approval of voretigene neparvovec (Luxturna®) for patients with biallelic RPE65 mutation-associated inherited retinal dystrophy with viable retinal cells represents an important step in the development of ocular gene therapies. Herein, we review studies investigating the episomal persistence of different recombinant adeno-associated virus (rAAV) vector genomes and the preclinical and clinical evidence of long-term effects of different RPE65 gene replacement therapies. A targeted review of articles published between 1974 and January 2021 in Medline®, Embase®, and other databases was conducted, followed by a descriptive longitudinal analysis of the clinical trial outcomes of voretigene neparvovec. Following an initial screening, 14 publications examining the episomal persistence of different rAAV genomes and 71 publications evaluating gene therapies in animal models were included. Viral genomes were found to persist for at least 22 months (longest study follow-up) as transcriptionally active episomes. Treatment effects lasting almost a decade were reported in canine disease models, with more pronounced effects the earlier the intervention. The clinical trial outcomes of voretigene neparvovec are consistent with preclinical findings and reveal sustained results for up to 7.5 years for the full-field light sensitivity threshold test and 5 years for the multi-luminance mobility test in the Phase I and Phase III trials, respectively. In conclusion, the therapeutic effect of voretigene neparvovec lasts for at least a decade in animal models and 7.5 years in human subjects. Since retinal cells can retain functionality over their lifetime after transduction, these effects may be expected to last even longer in patients with a sufficient number of outer retinal cells at the time of intervention.

  PublisherDOI

• A Systematic Review of Optogenetic Vision Restoration: History, Challenges, and New Inventions from Bench to Bedside

  Cold Spring Harbor Perspectives in Medicine · 2022-11-14 · 14 citations

  reviewOpen accessSenior author

  Blindness due to rod-cone dystrophies is a significant comorbidity and cause of reduced quality of life worldwide. Optogenetics uses adeno-associated viral (AAV) vectors to bypass lost photoreceptors and transfect remnant cell populations of the degenerated retina aiming to restore vision via the ectopic expression of opsins. The optogenetic targeting of retinal ganglion cells (RGCs) has been remarkably successful and several studies have advanced to clinical trials over the recent years. The inner retina and specifically ON bipolar cells represent even more appealing targets due to their intrinsically coded tasks in parallel processing and fine-tuning of visual signals before reaching the output: RGCs. However, present success with pursuing inner and outer retinal cells for optogenetic vision restoration is limited by multiple factors, including AAV tropism, promoter specificity, and retinal morphofunctional remodeling. Here we provide a review of the evolution of optogenetics, its greatest challenges, and solutions from bench to bedside.

  PublisherOA PDFDOI

• Photopharmacology for vision restoration

  Current Opinion in Pharmacology · 2022-06-21 · 18 citations

  reviewOpen access

  Blinding diseases that are caused by degeneration of rod and cone photoreceptor cells often spare the rest of the retinal circuit, from bipolar cells, which are directly innervated by photoreceptor cells, to the output ganglion cells that project axons to the brain. A strategy for restoring vision is to introduce light sensitivity to the surviving cells of the retina. One approach is optogenetics, in which surviving cells are virally transfected with a gene encoding a signaling protein that becomes sensitive to light by binding to the biologically available chromophore retinal, the same chromophore that is used by the opsin photo-detectors of rods and cones. A second approach uses photopharmacology, in which a synthetic photoswitch associates with a native or engineered ion channel or receptor. We review these approaches and look ahead to the next generation of advances that could reconstitute core aspects of natural vision.

  PublisherDOI

• Restoration of high-sensitivity patterned vision in motion with an engineered light-gated G protein-coupled receptor

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-04-09 · 1 citations

  preprintOpen access

  Abstract Inherited retinal degenerations (IRDs) result in blindness due to apoptotic cell death of rods and cones, but spare other retinal neurons, providing a potential that delivery of a light-activated signaling protein to surviving neurons may restore vision. We previously demonstrated that aspects of vision could be restored by introduction into surviving cells of a G protein-coupled receptor for glutamate (mGluR) bearing a tethered photoswitchable agonist. However, this system, containing one photoswitchable agonist per glutamate binding site, yielded low sensitivity, responding only to visual stimuli at the intensity of bright outdoor light, similar to channelrhodopsins. To increase sensitivity, we designed a multi-branched photoswitch, bearing four light-activatable glutamates for each glutamate binding site. When tethered to a modified mGluR2 expressed in retinal ganglion cells via intravitreal AAV gene delivery, this photoswitch boosted sensitivity by ~100-fold compared to the unbranched (single photo-ligand) photoswitch. This improvement in sensitivity enabled an IRD mouse model ( rd1 ) to perform visually-guided object recognition under incidental room light and pattern recognition using standard LCD computer displays. The restored line pattern differentiation approached the acuity reported for normal mouse vision. Pattern recognition functioned as well as wildtype vision with line patterns moving at speeds of up to 36°/s. In summary, this two-component chemical-optogenetic approach combines high sensitivity and high acuity with superior motion vision, and, unlike optogenetic gene therapy, can be adjusted for dose, upgraded, as new photoswitches are developed, and discontinued at will.

  PublisherOA PDFDOI

• Targeting ON-bipolar cells by AAV gene therapy stably reverses <i>LRIT3</i> -congenital stationary night blindness

  Proceedings of the National Academy of Sciences · 2022-03-22 · 29 citations

  articleOpen access

  Significance Canine models of inherited retinal diseases have helped advance adeno-associated virus (AAV)–based gene therapies targeting specific cells in the outer retina for treating blinding diseases in patients. However, therapeutic targeting of diseases such as congenital stationary night blindness (CSNB) that exhibit defects in ON-bipolar cells (ON-BCs) of the midretina remains underdeveloped. Using a leucine-rich repeat, immunoglobulin-like and transmembrane domain 3 ( LRIT3 ) mutant canine model of CSNB exhibiting ON-BC dysfunction, we tested the ability of cell-specific AAV capsids and promotors to specifically target ON-BCs for gene delivery. Subretinal injection of one vector demonstrated safety and efficacy with robust and stable rescue of electroretinography signals and night vision up to 1 y, paving the way for clinical trials in patients.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01EY008980

  NIH · $342k · 1997

• Directed Evolution of Adeno-Associated Virus for Retinal Gene Therapy

  NIH · $2.1M · 2014–2019

• NIH Grant R01EY013533

  NIH · $2.4M · 2007

• NIH Grant R01EY024958

  NIH · $2.2M · 2019

• Optogenetic Vision Restoration

  NIH · $1.6M · 2018–2022

Frequent coauthors

• Meike Visel

  55 shared

• Deniz Dalkara

  Inserm

  55 shared

• David V. Schaffer

  University of California, Berkeley

  53 shared

• William W. Hauswirth

  University of Florida

  49 shared

• Leah C. Byrne

  University of Pittsburgh

  43 shared

• José‐Alain Sahel

  Fondation Ophtalmologique Adolphe de Rothschild

  39 shared

• Kenneth P. Greenberg

  37 shared

• Scott Geller

  35 shared

Education

• Ph.D., biology

  University of California Santa Barbara

  1982