Tag Archives: Bryan Jones

Inner-Retinal Changes In AMD: Evidence, Mechanisms, and Future Perspectives

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We have a new manuscript out in Progress in Retinal Eye Research, Inner-retinal changes in AMD: Evidence, mechanisms, and future perspectives.

Authors: Matt Trinh , Michael Kalloniatis , Bryan William Jones @bwjones.bsky.social, Glenn C Yiu, Enrico Borrelli, Lisa Nivison-Smith.

Abstract: Age-related macular degeneration (AMD) has traditionally been regarded as a disorder of the outer-retina and choroid, characterised by drusen accumulation, retinal pigment epithelium (RPE) dysfunction, and photoreceptor degeneration. However, increasing evidence of inner-retinal involvement across the AMD spectrum, with structural and functional compromise evident from the early stages of disease, challenges this paradigm. Advances in spatially optimised optical coherence tomography (OCT), OCT angiography (OCTA), and high-resolution histology have revealed neuronal, vascular, and glial alterations within the inner-retina that reshape our understanding of AMD pathogenesis. This review synthesises clinical and experimental evidence on inner-retinal changes in AMD, including layer-specific thinning, microvascular rarefaction, impaired neurovascular coupling, and reactive gliosis. Such changes frequently emerge in early AMD, may precede, parallel, or exacerbate outer-retinal degeneration, and are associated with visual dysfunction not fully explained by photoreceptor loss alone. Importantly, mechanistic interactions between inner- and outer-retinal pathology support a bidirectional model of neurodegeneration, wherein region-specific vulnerability is shaped by perfusion dynamics, metabolic demands, and structural connectivity throughout the retina. Recognition of these processes expands the potential for earlier diagnosis, refined monitoring, and novel therapeutic targeting. By integrating structural, functional, and systemic insights, this review reframes AMD as a multi-layer neurovascular disease and underscores the central role of inner-retinal integrity in future AMD research and management.

Single-Cell Profiling of Trabecular Meshwork Identifies Mitochondrial Dysfunction In a Glaucoma Model That Is Protected By Vitamin B3 Treatment

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We have a new collaborative paper out in eLife: Single-Cell Profiling of Trabecular Meshwork Identifies Mitochondrial Dysfunction In a Glaucoma Model That Is Protected By Vitamin B3 Treatment.

Authors: Nicholas Tolman, Taibo Li, Revathi Balasubramanian, Guorong Li, Rebecca L. Pfeiffer@beccapfeiffer.bsky.social, Violet Bupp-Chickering, Ruth A Kelly, Marina Simón, John Peregrin, Christa Montgomery, Bryan Jones @bwjones.bsky.social, W Daniel Stamer, Jiang Qian, Simon WM John

Abstract: Since the trabecular meshwork (TM) is central to intraocular pressure (IOP) regulation and glaucoma, a deeper understanding of its genomic landscape is needed. We present a multi-modal, single-­ cell resolution analysis of mouse limbal cells (includes TM). In total, we sequenced 9,394 wild-­ type TM cell transcriptomes. We discovered three TM cell subtypes with characteristic signature genes validated by immunofluorescence on tissue sections and whole-­ mounts. The subtypes are robust, being detected in datasets for two diverse mouse strains and in independent data from two institutions. Results show compartmentalized enrichment of critical pathways in specific TM cell subtypes. Distinctive signatures include increased expression of genes responsible for (1) extracellular matrix structure and metabolism (TM1 subtype), (2) secreted ligand signaling to support Schlemm’s canal cells (TM2), and (3) contractile and mitochondrial/metabolic activity (TM3). ATAC-­ sequencing data identified active transcription factors in TM cells, including LMX1B. Mutations in LMX1B cause high IOP and glaucoma. LMX1B is emerging as a key transcription factor for normal mitochondrial function, and its expression is much higher in TM3 cells than other limbal cells. To understand the role of LMX1B in TM function and glaucoma, we single-­ cell sequenced limbal cells from Lmx1bV265D/+mutant mice (2491 TM cells). In Lmx1bV265D/+ mice, TM3 cells were uniquely affected by pronounced mitochondrial pathway changes. Mitochondria in TM cells of Lmx1bV265D/+ mice are swollen with a reduced cristae area, further supporting a role for mitochondrial dysfunction in the initiation of IOP elevation in these mice. Importantly, treatment with vitamin B3 (nicotinamide), which enhances mitochondrial function and metabolic resilience in other contexts, significantly protected Lmx1b mutant mice from IOP elevation.

Retinal Connectomics: A Review

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We have a new manuscript out of the lab in Volume 10 of the Annual Review of Vision Science titled Retinal Connectomics: A Review by Crystal L. Sigulinsky, Rebecca L. Pfeiffer, and Bryan William Jones. A .pdf is here.

Abstract
The retina is an ideal model for understanding the fundamental rules for
how neural networks are constructed. The compact neural networks of
the retina perform all of the initial processing of visual information be-
fore transmission to higher visual centers in the brain. The field of retinal
connectomics uses high-resolution electron microscopy datasets to map
the intricate organization of these networks and further our understand-
ing of how these computations are performed by revealing the fundamental
topologies and allowable networks behind retinal computations. In this ar-
ticle, we review some of the notable advances that retinal connectomics
has provided in our understanding of the specific cells and the organi-
zation of their connectivities within the retina, as well as how these are
shaped in development and break down in disease. Using these anatomi-
cal maps to inform modeling has been, and will continue to be, instrumental
in understanding how the retina processes visual signals.

Mitochondrial Transfer Between Inner Retinal Neurons

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This abstract was presented today, April 26th at the 2023 Association for Research in Vision and Opthalmology (ARVO) meetings in New Orleans, Louisiana by Selena Wirthlin, Crystal Sigulinsky, James Anderson, and Bryan William Jones.

Full resolution version here.

Purpose
Intercellular mitochondrial transfer has been reported across a variety of cells and tissues under both physiological and pathological conditions. Such transfer has shown broad therapeutic potential. The effectiveness of this therapy, however, is limited by a lack of understanding of the cellular and molecular mechanisms. Here, the ultrastructural features of mitochondrial transfer between inner retinal neurons discovered through retinal connectomics analysis is shown.

Methods
Retinal Connectome 2 (RC2) was built by automated transmission electron microscopy at ultrastructural (2nm/pixel) resolution. RC2 is a 0.25mm diameter volume of retina obtained from a 5-month-old female C57BL/6J mouse. The Viking application was used to visualize and annotate inter- and intracellular features of interest in the connectome.

Results
Exploration of RC2 revealed material transfer between apposing neural processes within the OFF subliminal of the inner plexiform layer. The transferred material can be defined as a mitochondria, confirmed by the presence of crustae. At the transfer site, a short, electron-dense 140-nm diameter tube with a curved cap tightly associated with the inner mitochondrial membrane of one neuritis extends into a vacuole within the apposing neuritis formed by the plasma membranes of the two cells. Thin cytoskeletal components consistent with actin microfilaments extend into the mitochondrion. Morphology and synaptology of the acceptor cell confirm it is an Aii amacrine cell, while preliminary findings suggest the donor cell is a type of ON/OFF ganglion cell.

Conclusions
These findings demonstrate active mitochondrial transfer between different classes of endogenous inner retinal neurons and suggests it may represent an important component of tissue homeostasis in the retina. Features of this transfer differ from previously reported mitochondrial transfer between photoreceptors upon transplantation, which may indicate cell type- or context-dependent differences in the cellular or molecular mechanisms. Our findings demonstrate active mitochondrial transfer between different classes of endogenous inner retinal neurons and suggest it may represent an important component of tissue homeostasis in the retina. Features of this transfer differ from previous reports by the Wallace and Pearson groups of material transfer between photoreceptors upon transplantation through tunneling nanotubes (Ortin- Martinez et al., 2021; Kalargyrou et al., 2021), which may indicate cell type- or context-dependent differences in the cellular or molecular mechanisms. Understanding these mechanisms could serve as a catalyst for development of novel therapeutics for disease in the retina and beyond.

Current Perspective on Retinal Remodeling: Implications for Therapeutics

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We have a new paper out of the lab, a perspectives paper on Retinal Remodeling: Implications for Therapeutics. (pdf here).

Authors are Rebecca L. Pfeiffer @BeccaPfeiffer19, and Bryan W. Jones @BWJones.

Abstract: The retinal degenerative diseases retinitis pigmentosa and age-related macular degeneration are a leading cause of irreversible vision loss. Both present with progressive photoreceptor degeneration that is further complicated by processes of retinal remodeling. In this perspective, we discuss the current state of the field of retinal remodeling and its implications for vision-restoring therapeutics currently in development. Here, we discuss the challenges and pitfalls retinal remodeling poses for each therapeutic strategy under the premise that understanding the features of retinal remodeling in totality will provide a basic framework with which therapeutics can interface. Additionally, we discuss the potential for approaching therapeutics using a combined strategy of using diffusible molecules in tandem with other vision-restoring therapeutics. We end by discussing the potential of the retina and retinal remodeling as a model system for more broadly understanding the progression of neurodegeneration across the central nervous system.

Dynein Dysregulation Due to the Absence of NUDC leads to Mitochondrial Mislocalization and Dysfunction in Rod Photoreceptors

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This abstract was presented today, May 4th at the 2022  Association for Research in Vision and Opthalmology (ARVO) meetings in Denver, Colorado by Hailey Levi @drpepperis100, Meredith Hubbard, Mary Anne Garner, TJ Hollingsworth, Ke Jiang, Nat Nelson, Anushree Gade, Drue Benefield, Guoxin Ying, Wolfgang Baehr, Bryan Jones@BWJones, Anand Swaroop, Glenn Rowe, and Alecia Gross @alecia144g.

Purpose: Mitochondrial stress impairs the function of photoreceptors and can lead to retinal degeneration and blindness. Microtubules and the cytoplasmic dynein complex are necessary for proper trafficking and localization of cargo, including mitochondria. We have identified Nuclear Distribution Protein C (NUDC), a known regulator of cytoplasmic dynein, to be critical in rod and cone photoreceptor health. We hypothesize that the absence of NUDC causes a dysregulation in dynein movement along microtubules leading to mitochondrial and protein mislocalization, as well as cellular stress and cell death.

Methods: We generated a floxed Nudc mouse and bred it to the rod-specific Opsin-iCre75 mouse to produce Nudc+/- or Nudc-/- in rods. To characterize the effect of NUDC loss on mitochondria in the retina of these mice, we performed a combination of assays including: Optical Coherence Tomography (OCT) to uncover retinal thickness in vivo; Transmission Electron Microscopy (TEM) to investigate the ultrastructure of mitochondria in rods; quantitative RT-PCR (qRT-PCR) to measure changes in transcripts of selected mitochondrial genes; immunohistochemistry (IHC) to reveal localization of key proteins involved in phototransduction, mitochondrial fission/fusion, and unfolded protein response (UPR) pathways; and seahorse assays to assess mitochondrial respiration in freshly dissected ex vivo retinal tissues.

Results: At P21, OCT analysis revealed retinal degeneration progressing through P42. TEM demonstrated an increased number of mitochondria scattered throughout the inner segment in Nudc-/- rods, rather than localized in the ellipsoid as in wild type. qRT-PCR showed no change or decrease in mRNA levels of genes associated with mitochondrial fission, but IHC revealed an upregulation of gliosis via GFAP in Müller glia and rhodopsin mislocalization in photoreceptors in the absence of NUDC. Additionally, altered mitochondrial respiration and mitochondrial reserve capacity were observed with Nudc deletion in P21 rods.

Conclusions: We have demonstrated that, in the absence of NUDC, mitochondria are mislocalized and exhibit compromised function in rod photoreceptors. We detect an upregulation of proteins involved in the UPR and in the inflammatory response concomitant with retinal degeneration, underscoring the importance of microtubule trafficking by NUDC in the overall health of photoreceptors.

Proteomic changes in the lens of a congenital cataract mouse model lead to reduced levels of glutathione and taurine

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This abstract was presented today, May 4th at the 2022  Association for Research in Vision and Opthalmology (ARVO) meetings in Denver, Colorado by Sheldon Rowan @SheldonRowan, Eloy Bejarano, Elizabeth Whitcomb, Rebecca Pfeiffer @BeccaPfeiffer19, Kristie Rose, Kevin Schey, Bryan Jones @BWJones, Allen Taylor.

Purpose: Congenital cataracts develop through multiple mechanisms, but often lead to common endpoints, including protein aggregation, impaired fiber cell differentiation, and absence of fiber cell denucleation. It is now apparent that other metabolic abnormalities associate with cataractogenesis, including reductions in levels of amino acids, glutathione, and taurine. Here, we analyze the proteome and metabolome of mice expressing a mutant ubiquitin protein (K6W-Ub) to determine the molecular mechanisms underlying formation of its congenital cataract.

Methods: C57BL/6J wild-type or cataractous K6W-Ub transgenic mouse lenses were dissected at E15.5, P1, or P30 and proteins were analyzed via MS-based tandem-mass-tag (TMT) quantitative proteomics. Small molecules were spatially quantified using computational molecular phenotyping (CMP), a tool that enables acquisition of free amino acid fingerprints for every cell in the lens. Validation of proteomics findings was also performed using Western blot analysis and immunohistochemistry.

Results: Proteomic analyses revealed pathways that were altered during lens differentiation, by expression of K6W-Ub, or both. Prominent pathways included glutathione metabolism; glycolysis/gluconeogenesis; and glycine, serine, and threonine metabolism. Within the glutathione metabolism pathway, GSTP1 and GGCT were most strongly downregulated by K6W-Ub. Other consistently downregulated proteins were PGAM2, GAMT, and HMOX1. Proteins that were upregulated by K6W-Ub expression belonged to pathways related to lysosome, autophagy, Alzheimer’s disease, and glycolysis/gluconeogenesis. Analysis of the metabolome via CMP revealed statistically significant decreases in taurine and glutathione and smaller decreases in glutamate, glutamine, aspartate, and valine in all ages of K6W-Ub lenses. Lens metabolites were spatially altered in the cataractous K6W-Ub lens.

Conclusions: K6W-Ub expressing lenses replicate many congenital cataract phenotypes and are useful disease models. The large reductions in levels of taurine and glutathione may be general signatures of cataract development, as human cataracts also have reduced glutathione and taurine. Key roles for amino acid metabolism and glycolysis/gluconeogenesis in cataractogenesis are emerging. Together our data point toward potential common metabolic/proteomic signatures of cataracts.