Transcriptome profiling from Wild Type and PLSCR1 transgenic mouse(PLSCR1-TG)retina with acute ocular hypertension (AOH) treatment reveals the potential mechanism involved in glaucoma
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ABSTRACT:
PROVIDER: PRJNA775966 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16611287_1.fastq.gz | Fastqsanger.gz | |||
| SRR16611287_2.fastq.gz | Fastqsanger.gz | |||
| SRR16611288_1.fastq.gz | Fastqsanger.gz | |||
| SRR16611288_2.fastq.gz | Fastqsanger.gz | |||
| SRR16611289_1.fastq.gz | Fastqsanger.gz |
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Project description:Glaucoma is a leading cause of irreversible blindness worldwide. In pathogenesis of glaucoma, the molecular mechanisms remain largely unknown. Phospholipid scramblase 1 (PLSCR1) is a key regulator promoting RGCs apoptosis and their clearance by microglia. As evidenced in RGCs of PLSCR1 transgenic mice model treated with acute ocular hypertension, transcriptome profiling from Wild Type and PLSCR1 transgenic mouse(PLSCR1-TG)retina with AOH treatment would reveal the potential mechanism involved in glaucoma.
2023-09-11 | GSE186750 | GEO
Project description:Purpose: The optic nerve head (ONH) is the likely site of initial damage in the glaucomatous eye. Despite the recognition of elevated intraocular pressure (IOP) as a leading risk factor for the development of glaucoma, ocular hypertension (OHT) eyes displaying consistently elevated IOP do not experience ONH damage. This study aims to identify global gene expression variations in glaucomatous ONHs and their relationship to those identified in OHT derived ONHs in order to improve our understanding of IOP-induced ONH damage. Methods: (N=6) ONHs were collected from clinically confirmed glaucoma, OHT and age-matched control donor eyes. Total RNA extracted from ONHs was reverse transcribed and assayed using the Affymetrix Human Exon 1.0 ST array. Differentially expressed genes in glaucoma versus control and OHT derived ONHs were identified using an ANOVA analysis with a 1.25 fold change limit and P-value < 0.05. Quantitative RT-PCR was performed to validate selected differentially expressed genes. Results: Microarray analysis revealed 149 under under-expressed genes in POAG versus control ONHs, many of which are involved in ion transport, axonogenesis and macromolecule catabolic processes. 297 genes were over expressed in OHT versus glaucoma derived ONHs. Mediators of oxidation-reduction and chemical homeostasis were among the most prominent gene groups identified. The over expression of prostaglandin-endoperoxide synthase 2, integrin, beta-like 1 and fibulin 5 in glaucomatous ONHs was confirmed by qRT-PCR. Conclusions: Our data demonstrates marked alteration in global gene expression patterns in the glaucomatous ONH, likely due to extensive tissue injury. The observed overlapping of several differentially expressed genes in glaucoma and OHT derived ONHs suggests the induction of common mechanisms in response to elevated IOP. Preferential over-expression of certain gene groups in OHT but not glaucoma derived ONHs may confer possible protection against IOP-induced ONH damage, which remains to be investigated in future studies. (N=6) Glaucoma, ocular hypertension and age-matched control ONHs were assayed to investigate and compare global gene expression patterns in each sample group.
2013-09-27 | E-GEOD-45570 | biostudies-arrayexpress
Project description:Glaucoma leads to vision loss due to retinal ganglion cell death. Astrocyte reactivity contributes to neurodegeneration. Our recent study found that lipoxin B4 (LXB4), produced by retinal astrocytes, has direct neuroprotective actions on retinal ganglion cells. In this study, we aimed to investigate how the autacoid LXB4 influences astrocyte reactivity in the retina under inflammatory cytokine-induced activation and ocular hypertension conditions. The protective activity of LXB4 was investigatedin vivousing the mouse silicone-oil model of chronic ocular hypertension (n=40). By employing a range of analytical techniques, including bulk RNA-seq, RNAscope in-situhybridization, qPCR, and lipidomic analyses, we discovered the formation of neuroprotective lipoxins in rodents (including the retina and optic nerve), primates (optic nerve), and human brain astrocytes, indicating their presence across various species. Our findings in the mouse retina demonstrated significant dysregulation of the lipoxin pathway in response to chronic ocular hypertension, leading to an increase in 5-lipoxygenase (5-LOX) activity and a decrease in 15-lipoxygenase activity. This dysregulation was coincident with a marked upregulation of astrocyte reactivity. Reactive human brain astrocytes also showed a significant increase in 5-LOX. Administration of LXB4 regulated the lipoxin pathway, restored and amplified LXA4 generation (another lipoxin with distinct bioactions), and mitigated astrocyte reactivity in mouse retinas and human brain astrocytes. In conclusion, the lipoxin pathway is functionally expressed in rodents, primates, and human astrocytes, and is a resident neuroprotective pathway that is downregulated in reactive astrocytes. Novel cellular targets for LXB4’s neuroprotective action are inhibition of astrocyte reactivity and restoration of lipoxin generation. Amplifying the lipoxin pathway is a potential target to disrupt or prevent astrocyte reactivity in neurodegenerative diseases.
2024-04-10 | GSE241131 | GEO
Project description:Purpose: The optic nerve head (ONH) is the likely site of initial damage in the glaucomatous eye. Despite the recognition of elevated intraocular pressure (IOP) as a leading risk factor for the development of glaucoma, ocular hypertension (OHT) eyes displaying consistently elevated IOP do not experience ONH damage. This study aims to identify global gene expression variations in glaucomatous ONHs and their relationship to those identified in OHT derived ONHs in order to improve our understanding of IOP-induced ONH damage. Methods: (N=6) ONHs were collected from clinically confirmed glaucoma, OHT and age-matched control donor eyes. Total RNA extracted from ONHs was reverse transcribed and assayed using the Affymetrix Human Exon 1.0 ST array. Differentially expressed genes in glaucoma versus control and OHT derived ONHs were identified using an ANOVA analysis with a 1.25 fold change limit and P-value < 0.05. Quantitative RT-PCR was performed to validate selected differentially expressed genes. Results: Microarray analysis revealed 149 under under-expressed genes in POAG versus control ONHs, many of which are involved in ion transport, axonogenesis and macromolecule catabolic processes. 297 genes were over expressed in OHT versus glaucoma derived ONHs. Mediators of oxidation-reduction and chemical homeostasis were among the most prominent gene groups identified. The over expression of prostaglandin-endoperoxide synthase 2, integrin, beta-like 1 and fibulin 5 in glaucomatous ONHs was confirmed by qRT-PCR. Conclusions: Our data demonstrates marked alteration in global gene expression patterns in the glaucomatous ONH, likely due to extensive tissue injury. The observed overlapping of several differentially expressed genes in glaucoma and OHT derived ONHs suggests the induction of common mechanisms in response to elevated IOP. Preferential over-expression of certain gene groups in OHT but not glaucoma derived ONHs may confer possible protection against IOP-induced ONH damage, which remains to be investigated in future studies.
2013-09-27 | GSE45570 | GEO
Project description:Experimental ocular hypertension (IOP) induces senescence of retinal ganglion cells (RGCs) that mimicks events occurring in human glaucoma. An established transgenic p16-3MR mouse model in which the systemic administration of the small molecule ganciclovir (GCV) selectively kills p16INK4a-expressing cells was used to compare transcriptomes of retinas from IOP and control eyes in GCV-treated and non-treated mice, to investigate how experimental removal of senescent p16INK4a-positive cells impacts retinal cells in conditions resembling glaucoma.
2020-12-01 | GSE141725 | GEO
Project description:The resident astrocytes-retinal ganglion cell lipoxin circuit is impaired during retinal stress that include exocytotoxic- and ocular hypertension-induced neuropathy. Two endogenous lipoxins (Lipoxin A4 and Lipoxin B4) produced by homeostatic astrocytes directly act on RGCs. LXB4 is the most potent lipoxin in the retina and directly increases RGC survival and function in ocular hypertension-induced neuropathy. Homeostatic roles and cellular targets of LXB4 in the retina and optic nerve are a critical gap in knowledge. Single-cell RNA sequencing was used to define cellular targets and signaling of LXB4 in the retina. For modeling neurodegeneration, sustained ocular hypertension was induced by silicone-oil injection in the anterior chamber of mouse eyes. For morphological characterization of microglia populations in the retina and optic nerve, we used MorphOMICs and pseudotime trajectory analysis. Bulk RNA sequencing of optic nerves was performed to characterize pathways and mechanism of action for LXB4. qPCR and immunohistochemistry were used for validation of transcriptomics data. Student’s t-test and one-way ANOVA were used to determine differences between experimental groups. Single Cell transcriptomic identified microglia as a primary target for LXB4 in the healthy retina. LXB4 downregulated genes that drive microglia environmental sensing and reactivity responses. Analysis of microglia function uncovered that ocular hypertension induces distinct, temporally defined and dynamic phenotypes in the retina and, unexpectedly, in the distal myelinated optic nerve. Microglial expression of CD74, a marker of disease-associated microglia (DAM) in the brain, was only induced in a unique population of optic nerve microglia but not the retina. Genetic deletion of lipoxin formation correlated with presence of a CD74 optic nerve microglia population in normotensive eyes optic, while LXB4 treatment during ocular hypertension shifted optic nerve microglia toward a homeostatic morphology and non-reactive state and downregulated expression of CD74. Furthermore, we identified a correlation between CD74 and phospho-PI3K (p-PI3K) expression levels in the optic nerve, that was reduced by LXB4 treatment. Results identify distal optic nerve microglial dynamic and reactive responses as a key feature of ocular hypertension induce neurodegeneration. Our findings establish microglia regulation as a new LXB4 cell target in the retina and optic nerve. LXB4 maintenance of optic nerve microglia homeostatic phenotype and inhibition of a disease-associated phenotype are potential mechanisms for LXB4 neuroprotection.
2024-04-10 | GSE251716 | GEO
Project description:The resident astrocytes-retinal ganglion cell lipoxin circuit is impaired during retinal stress that include exocytotoxic- and ocular hypertension-induced neuropathy. Two endogenous lipoxins (Lipoxin A4 and Lipoxin B4) produced by homeostatic astrocytes directly act on RGCs. LXB4 is the most potent lipoxin in the retina and directly increases RGC survival and function in ocular hypertension-induced neuropathy. Homeostatic roles and cellular targets of LXB4 in the retina and optic nerve are a critical gap in knowledge. Single-cell RNA sequencing was used to define cellular targets and signaling of LXB4 in the retina. For modeling neurodegeneration, sustained ocular hypertension was induced by silicone-oil injection in the anterior chamber of mouse eyes. For morphological characterization of microglia populations in the retina and optic nerve, we used MorphOMICs and pseudotime trajectory analysis. Bulk RNA sequencing of optic nerves was performed to characterize pathways and mechanism of action for LXB4. qPCR and immunohistochemistry were used for validation of transcriptomics data. Student’s t-test and one-way ANOVA were used to determine differences between experimental groups. Single Cell transcriptomic identified microglia as a primary target for LXB4 in the healthy retina. LXB4 downregulated genes that drive microglia environmental sensing and reactivity responses. Analysis of microglia function uncovered that ocular hypertension induces distinct, temporally defined and dynamic phenotypes in the retina and, unexpectedly, in the distal myelinated optic nerve. Microglial expression of CD74, a marker of disease-associated microglia (DAM) in the brain, was only induced in a unique population of optic nerve microglia but not the retina. Genetic deletion of lipoxin formation correlated with presence of a CD74 optic nerve microglia population in normotensive eyes optic, while LXB4 treatment during ocular hypertension shifted optic nerve microglia toward a homeostatic morphology and non-reactive state and downregulated expression of CD74. Furthermore, we identified a correlation between CD74 and phospho-PI3K (p-PI3K) expression levels in the optic nerve, that was reduced by LXB4 treatment. Results identify distal optic nerve microglial dynamic and reactive responses as a key feature of ocular hypertension induce neurodegeneration. Our findings establish microglia regulation as a new LXB4 cell target in the retina and optic nerve. LXB4 maintenance of optic nerve microglia homeostatic phenotype and inhibition of a disease-associated phenotype are potential mechanisms for LXB4 neuroprotection.
2024-04-10 | GSE250615 | GEO
Project description:Background: the major risk factor for glaucoma is ocular hypertension, a disorder caused by reduced outflow of aqueous humor through the trabecular meshwork. In a previous pharmacogenomic screen for genes associated with ocular hypertension, we identified the novel G protein-coupled receptor, GPR158, and showed it protects against age-related ocular hypertension in mice. Here we show that the glucocorticoid, dexamethasone, increases the level of accumulated GPR158 protein in the trabecular meshwork of the human eye, ex vivo. Methods: we performed gene expression microarray profiling of TM-1 cells thar overexpress GPR158 Results: we show that the glucocorticoid, dexamethasone, increases the level of accumulated GPR158 protein in the trabecular meshwork of the human eye, ex vivo. Gene sets controlled by dexamethasone, TGFB1 and TP53 were identified, as well as genes asso-ciated with ossification. GPR158 over-expression in cells of the immortalized trabecular meshwork cell line TM-1 did not affect the fibrotic response to dexamethasone or cause ossification, and loss of GPR158 in knockout mice did not affect the development of glucocorticoid-induced ocular hypertension. However, GPR158 over-expression was cytoprotective. Discussion: Our findings suggest that GPR158 activated the cytoprotective branch of the unfolded protein response and bound the TP53-inducible protein PPP1R10, a regulatory subunit of PPI regulatory subunit of PPI. Our data support the idea that GPR158 protects the trabecular meshwork, and suggest possible mechanisms.
2024-06-30 | GSE236016 | GEO
Project description:Elevated intraocular pressure is considered a major cause of glaucomatous retinal neurodegeneration. To facilitate a better understanding of the underlying molecular processes and mechanisms, we report a study focusing on alterations of the retina proteome by induced ocular hypertension in a rat model of the disease. Glaucomatous processes were modelled through sclerosing the aqueous outflow routes of the eyes by hypertonic saline injections into an episcleral vein. Mass spectrometry-based quantitative retina proteomics using a label-free shotgun methodology identified over 200 proteins significantly affected by ocular hypertension. Various facets of glaucomatous pathophysiology were revealed through the organization of the findings into protein interaction networks and by pathway analyses. Concentrating on retinal neurodegeneration as a characteristic process of the disease, elevated intraocular pressure-induced alterations in the expression of selected proteins were verified by targeted proteomics based on nanoflow liquid chromatography coupled with nanoelectrospray ionization tandem mass spectrometry using the parallel reaction monitoring method of data acquisition. Acquired raw data are shared through deposition to the ProteomeXchange Consortium making a retina proteomics dataset on the selected animal model of glaucoma available for the first time.
2023-10-24 | PXD042729 | Pride
Project description:<p>The Ocular Hypertension Treatment Study (OHTS) is an National Eye Institute-sponsored multi-center, randomized, prospective treatment trial designed to determine whether lowering intraocular pressure (IOP) in individuals with ocular hypertension delays or prevents the development of primary open angle glaucoma (POAG). A total of 1,636 individuals with ocular hypertension between 40 and 80 years old were enrolled in the study. In addition to ocular hypertension, subjects in the OHTS were required to have normal optic nerve appearance as determined by the OHTS Optic Disc Reading Center and normal and reliable visual field tests at the time of enrollment by the OHTS Visual Field Reading Center. OHTS subjects were randomly assigned to either an observational group which received close observation or a topical medication group which received medication as needed to achieve a 20% reduction in IOP from their baseline levels. Subjects then were examined at regular intervals for optic disc cupping or visual field defects. Other clinical measures were also obtained from OHTS subjects including central corneal thickness (CCT) and intraocular pressure. The primary outcome monitored for the OHTS was the development of glaucoma in one or both eyes as defined by reproducible visual field abnormality or reproducible optic disc deterioration attributed to POAG by the masked OHTS Endpoint Committee. The OHTS study design has been reported in detail (Gordon, 1999; PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/10326953" target="_blank">10326953</a>).</p> <p>The OHTS confirmed that ocular hypertension is a risk factor for developing POAG and showed that lowering IOP reduced the risk for developing POAG (Kass, 2002; PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/12049574" target="_blank">12049574</a>). The OHTS also demonstrated that thin CCT is a significant risk factor for the development of POAG (Gordon, 2002; PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/12049575" target="_blank">12049575</a>).</p> <p>Blood samples were also collected from 1,077 OHTS participants for an ancillary genetics study. DNA was prepared from these samples and used in a genome-wide association scan (GWAS) designed to identify genetic factors that control the magnitude of quantitative features of glaucoma (baseline IOP, baseline cup-to-disc ratio, and CCT). Genotypes from the GWAS and these clinical data (IOP, cup-to-disc ratio, and CCT) have been provided to dbGaP.</p>
| phs000240 | dbGaP