RNA-seq of human iPS cell-derived retinal ganglion cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE326418 | GEO | 2026/08/10
REPOSITORIES: GEO
Similar Datasets
Project description:Goals of the study: 1. Assess the gene expression profile in rat RGC after experimental IOP elevation to elucidate the molecular mechanisms of RGC death. 2. Identify potentially novel genes and pathways that may contribute to RGC death in glaucoma. Background: Glaucoma is a neurodegenerative disease characterized by the slow, progressive degeneration of RGC. Elevated IOP is the biggest risk factor for developing glaucoma, loss of RGC and optic nerve atrophy. The pathophysiology of glaucomatous neurodegeneration is not fully understood. It is now clear that RGC die by apoptosis in glaucoma. However, what triggers the apoptosis is still unknown. So far, several gene expression studies have been performed on the retina as a whole. These studies revealed up and downregulation of many genes in response to elevated IOP and optic nerve transection. However, the retina is a complex tissue composed of neuronal, glial and vascular cell types. The RGCs only comprise 5% or less of retinal cells. The gene expression profiles from whole retina can not represent of RGC gene expression. In the current study, we sought to investigate the whole genome regulation of the RGCs in glaucoma. The study was carried out in 3 adult male Brown Norway rats with experimental glaucoma. An equal number of RGCs were captured from normal eyes and eyes with elevated IOP. Gene expression in the glaucomatous RGC was compared with that in the fellow RGC by using Affymetrix Gene chip.
2010-10-01 | E-GEOD-12596 | biostudies-arrayexpress
Project description:The neuronal cell death results in neurodegenerative diseases. The extracellular environment plays a critical role in regulating cell viability. In this study, we explore how intercellular communication contributes to the survival of retinal ganglion cells (RGCs) following the optic nerve crush (ONC). By performing single-cell RNA-seq on whole retinal cells, we observed transcriptomic responses in non-RGC retinal cells to the injury, with astrocytes and Müller glia having the most interactions with RGCs. By comparing the RGC subclasses showing distinct resilience cell death, we identified top 47 interactions that are stronger in the high-survival RGCs, likely representing neuroprotective interactions. We performed functional assays on one of the receptors, Mu-opioid receptor (Oprm1). Although Oprm1 is preferentially expressed in intrinsically photosensitive retinal ganglion cells (ipRGCs), its neuroprotective effect could be transferred to multiple RGC subclasses by specific overexpressing Oprm1 in pan-RGCs. Our study provides an atlas of cell-cell interactions in both intact and post-ONC retina and an effective strategy to predict molecular mechanisms in neuroprotection, underlying the principal role played by extracellular environment in supporting neuron survival.
2023-10-01 | GSE241268 | GEO
Project description:Retinal ganglion cells (RGCs) are the sole projection neurons that connect the eye with the brain, and the degeneration of these cells in diseases such as glaucoma results in vision loss or blindness. Similar to other neurons throughout the central nervous system, RGCs are postmitotic and therefore highly dependent upon autophagy to remove damaged proteins or organelles to maintain proper cellular homeostasis. Autophagy deficits have been implicated in multiple neurodegenerative diseases including glaucoma. In addition, a subpopulation of glaucoma patients possesses mutations in the autophagy receptor Optineurin (OPTN) resulting glaucoma within a normal range of intraocular pressure, with the OPTN(E50K) mutation known to induce a severe degeneration. Despite this, our knowledge of how autophagy impairment promotes neurodegeneration within RGCs remains limited. We advanced a human pluripotent stem cell (hPSC) model of RGC neurodegeneration with an underlying OPTN(E50K) mutation to study how autophagy disruption contributes to RGC neurodegeneration. We identified OPTN protein was reduced but accumulated within the somas in RGCs with the OPTN(E50K) mutation, and this accumulation was associated with a decrease in autophagic flux. To rule out the possibilities that the specificity of the antibody incapable to recognize E50K region resulting the reduction of OPTN protein, we performed proteomics analysis at week 2 hPSC-RGCs of post purification and identified 154 downregulated proteins as well as 178 upregulated proteins associated with OPTN(E50K) RGCs compared with isogenic controls. Taken together, we identified proteins that were altered by OPTN(E50K) mutation in RGCs, and which may provide potential mechanisms that contribute to RGC neurodegeneration.
2025-05-06 | PXD033173 | Pride
Project description:Optic neuropathies, including glaucoma, are characterized by the progressive degeneration of retinal ganglion cells (RGCs), ultimately leading to irreversible vision loss. Increasing evidence implicates microglia, the resident immune cells of the central nervous system, as key modulators of RGC health and disease progression. However, the precise mechanisms by which microglia influence RGCs remain poorly understood, particularly in the human context. In this study, we established human pluripotent stem cell (hPSC)-derived co-culture systems incorporating microglia, astrocytes, and RGCs to explore how microglia shape RGC growth and maturation under physiological conditions. We first examined the impact of homeostatic microglia on RGCs in both co-culture and tri-culture systems, revealing distinct influences of cell types in co-culture compared to when they were grown individually. We then modeled inflammatory states by activating microglia with lipopolysaccharide (LPS) and evaluated their effects on RGCs both directly and in the context of astrocyte co-culture. This stepwise, reductionist approach enabled us to dissect the cellular interactions driving RGC vulnerability in inflammatory conditions relevant to optic neuropathies. Our findings provide new insight into the complex neuroimmune landscape that underlies RGC degeneration and identify key pathways that may serve as therapeutic targets across a range of optic nerve diseases
2025-09-20 | GSE308054 | GEO
Project description:Retinal ganglion cells (RGCs) play a critical role in the transmission of visual signals from the retina to the brain required for proper vision. The optic neuropathies, including glaucoma, NAION, LHON, traumatic optic neuropathy, optic pathway glioma result in the reversible and irreversible changes in RGCs, ultimately leading to their death. RGC loss is permanent given that these cells cannot regenerate in mammals. Neuroregenerative strategies for managing optic neuropathies have mainly focused on restoring the lost RGC cell population in a glaucomatous retina. This treatment approach not only aims to halt disease progression, but also to restore the lost vision by replacing the damaged/lost RGCs through RGC transplantation. Significant strides have been made in this field of RGC transplantation and regeneration. As a first step of RGC transplantation, several protocols now exist to differentiate cells into primary RGCs, and several sources of donor RGC have been established including human ES and iPSC-derived RGCs. To achieve functional regeneration, the transplanted RGCs must survive, integrate, and extend their axons and establish connections within the retina and the brain. Of the many factors influencing initial donor RGCs survival, the innate immunity [ref] and primarily microglia reactivity is of particular interest. In ocular models of glaucoma, microglia have been heavily implicated in driving disease progression, promoting a pro-inflammatory environment. In some instances, activated microglia have been directly implicated in RGC loss by mediating phagocytosis of the damaged or injured RGCs. In line with this, our recent work, shows that activated host microglia are detrimental to donor RGCs, presumably via phagocytosis of the donor RGCs. We observed that pre-treatment of donor RGCs with FasL and annexin V to block the exposed phosphatidylserine residues of the stressed donor RGCs prior to transplantation reduced activation of host microglia, and better RGC survival rates post transplantation. Studies like these and others underscore the importance of modulating host microglia reactivity for better transplantation outcomes. To further improve donor RGC survival post transplantation, a better understanding of the host myeloid cell reactivity following donor RGC transplantation is paramount. We and others have previously shown the importance of modulating the retinal microenvironment to promote RGC survival. In the current study, we profiled the transcriptome of the host myeloid cell population (CX3CR1-GFP) using a single cell RNA sequencing approach, to delineate the myeloid cell population most relevant for donor RGC survival post transplantation. A focused analysis on the microglia cell population was performed, given their established role in glaucoma disease progression. In addition to profiling the expression pattern of the known classic microglia disease associated signatures such as ApoE, Spp1, and Lgals, we identified several other genes associated with, and or driving microglia activation, including Cybb, Atf3, Aurka and Kif22. Given the known function of these genes in other disease contexts, we believe that these genes are important for modulating donor RGC survival post transplantation, thus warrant further investigation in this context. Taken together, with reference to our established adult mouse retina cell atlas, we present a comprehensive analysis of the host myeloid cell population, specifically focusing on microglia reactivity status, at a single cell resolution level, providing insights into the regulatory mechanisms that may be important for donor RGC survival and integration into glaucomatous retina post transplantation.
2025-12-12 | GSE285564 | GEO
Project description:RGC differentiation is tightly controlled by extrinsic and intrinsic factors. Growth and differentiation factor 15 (GDF-15) promotes RGC differentiation, opposite to GDF-11 which inhibits RGC differentiation, both in the mouse retina and in human stem cells. To deepen our understanding of how these two closely related molecules confer opposing effects on retinal development, here we assess the transcriptional profiles of mouse retinal progenitors exposed to exogenous GDF-11 or -15. We find a dichotomous effect of GDF-15 on RGC differentiation, decreasing RGCs expressing residual pro-proliferative genes and increasing RGCs expressing non-proliferative genes, suggestive of greater RGC maturation. Furthermore, GDF-11 promoted the differentiation of photoreceptors and amacrine cells. These data enhance our understanding of the mechanisms underlying the differentiation of RGCs and photoreceptors from retinal progenitors and suggest new approaches to the optimization of protocols for the differentiation of these cell types.
2024-05-16 | GSE252861 | GEO
Project description:Retinal ganglion cells (RGCs) are the projection neurons of the retina. Proper development of the axon and dendrite of RGCs is the basis for these cells to function as projection neurons to deliver visual information to the brain. The purpose of this study was to investigate the function of a newly identified RGC-specific gene, Shtn1, in neurite development in RGCs. Using IF, we demonstrated that SHTN1 is distinctively expressed in RGCs during the period in which RGCs actively develop and adjust the connections of their neurites with upstream and downstream neurons. Using the iRGC system, we demonstrated that Shtn1 promotes the growth and complexity of neurites, and thus the electrophysiological maturation, of iRGCs. RNA-Seq analyses showed that Shtn1 may also regulate gene expression and neurogenesis in iRGCs. These findings improve our understanding of the molecular machinery governing RGC neurite development, and may help to optimize future RGC regeneration methods.
2024-07-10 | GSE254839 | GEO
Project description:Background: As the sole output neurons for the retina, retinal ganglion cells (RGCs) transmit all visual information from the retina via the optic nerve to the brain. RGCs do not regenerate when injured, and effective therapies for promoting RGC survival and axon regeneration in optic neuropathies comprise an unmet clinical need, including in the common disease glaucoma. Histone deacetylases (HDACs) are epigenetic modifiers that repress gene transcription and play a key role in retinal development and disease. In this study, we identify the role of HDAC4 in RGC neurodegeneration and axon regeneration. Methods: The role of HDAC4 in the regulation of RGC neuroprotection and axon regeneration was studied in the mouse optic nerve crush (ONC) model for optic neuropathy by transduction of RGCs in vivo with adeno-associated virus (AAV) vectors. HDAC4- and ONC-dependent gene expression in vivo were studied by single cell RNA sequencing (scRNA-seq) of isolated RGCs. Results: A loss-of-function screen for the role of HDACs in RGC survival after optic nerve crush (ONC) injury identified HDAC4 as essential element for RGC survival. Accordingly, expression of a constitutively nuclear HDAC4 S246/467/632A missense mutant (3SA) increased RGC survival and axon regeneration after ONC injury. Similar beneficial effects were conferred by expression of an N-terminal fragment of HDAC4 (HDAC4 NT) that constitutively represses gene expression. scRNA-seq showed that one day after ONC injury, transcriptomic profiles of RGCs were altered such that HDAC4 NT and to a lesser degree the HDAC4 3SA mutant attenuated the gene expression changes associated with injury. Conclusions: This study demonstrates that enhancement of nuclear HDAC4 activity will promote RGC survival and axon regeneration in the ONC model of RGC injury, identifying HDAC4 as a novel target in the development of therapeutics for RGC protection and restoration of visual function.
2026-01-01 | GSE252860 | GEO
Project description:Since retinal ganglion cells (RGCs) do not regenerate after injury, RGC replacement therapy could provide an approach to vision restoration in glaucoma and other optic neuropathies. Here we developed a rapid protocol for direct induction of RGC (iRGC) differentiation from human iPSCs and ESCs in less than two weeks, by overexpression of NGN2 in RGC survival-promoting medium supplemented with a Notch inhibitor. Neuronal morphology and neurite growth were observed within one week of induction. Immunostaining and qRT-PCR for characteristic RGC-specific genes confirmed identity. Calcium imaging was used to evaluate iRGCs’ electrophysiologic maturation, and demonstrated GABA-induced excitatory calcium influx characteristic of immature RGCs. Using single cell-RNA sequencing (scRNA-seq) we further delineated iRGCs’ differentiation and compared iRGC transcriptomic profiles to fetal human and retinal organoid-derived RGCs. Unbiased clustering showed high similarities of transcriptomic profiles among iRGCs, early-stage fetal human RGCs and early-stage retinal organoid-derived RGCs. However, for some markers, including BRN3a, BRN3b and NEFL, iRGCs demonstrated expression patterns more similar to fetal RGCs than to retinal organoid RGCs. After intravitreal injection into rodent eyes, transplanted iRGCs survived and migrated into host retinas where they were detected one week and one month after transplant. Prior optic nerve trauma to the recipient host did not significantly enhance or detract from iRGC integration, but iRGCs protected host RGCs from neurodegeneration. Taken together, these data demonstrate rapid iRGC generation in vitro into an immature cell with high similarity to human fetal RGCs and capacity for retinal integration after transplant, including after optic nerve injury. The simplicity of this system may benefit translational studies on human RGCs.
2022-04-10 | GSE200452 | GEO
Project description:Retinal ganglion cells (RGCs) are the projection neurons that transmit visual information from the retina to the brain via the optic nerve. A substantial proportion of RGCs are eliminated by programmed cell death during development to regulate their final number, yet how cell death impacts RGC development in human retinas remains poorly understood. Here, we characterized the timing and cell-type-specificity of cell death in human fetal retinas and retinal organoids. We identified two waves of apoptosis: an early wave targeting retinal neuronal precursors and a late wave affecting RGCs and other neurons. In addition to these two waves of apoptosis, organoids displayed a distinct wave of necrosis in the innermost core region that eliminates nearly all RGCs during long-term culture. To investigate the functions of the apoptotic waves during retinal development, we differentiated BAX/BAK double mutant organoids that are deficient for apoptosis. In these mutant organoids, RGC survival was improved, RGC neurogenesis and maturation were delayed, and RGCs were lost through a compensatory increase in necrosis. Our data suggest that the waves of developmental apoptosis promote human RGC neurogenesis and maturation. Together, our results highlight the roles of cell death in human RGC development and the challenges in retinal organoid design. Overcoming these obstacles would improve the utility of retinal organoids for modeling optic neuropathies like glaucoma
2025-11-02 | GSE305194 | GEO