Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1050754 | ENA |
REPOSITORIES: ENA
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Project description:Mass spectrometry-based proteomics by bottom-up approaches enables the unbiased and sensitive profiling of cellular proteomes and extracellular environments. Recent technological and bioinformatic advances permit identifying of dual biological systems in a single experiment, supporting investigation of infection from the perspective of both a host and pathogen. At the ocular surface, P. aeruginosa are commonly associated with biofilm formation and inflammation of the ocular tissues, causing damage to the eye. The interaction between P. aeruginosa and the immune system at the site of infection describes limitations in clearance of infection and enhanced pathogenesis. Here, we profile the extracellular environment (eye wash) of murine ocular surfaces infected with a clinical isolate of P. aeruginosa and detect neutrophil marker proteins, indicating neutrophil recruitment to the site of infection. In addition, we define the deepest murine corneal proteome to date and detect proteins, categories, and networks critical to the host response to infection. Moreover, we provide the first identification of bacterial-specific proteins in response to the host during bacterial biofilm formation of the eye. We validate our findings through in silico comparisons and enzymatic profiling. Overall, our work provides comprehensive profiling of the host-pathogen interface and uncovers differences between general and site-specific host responses to infection.
2020-01-09 | PXD015362 | Pride
Project description:We successfully induced corneal epithelial cells from human iPSCs. Then, we perfomed global expression analysis using microarray to compare the character of hiPSC-derived corneal epithelial cells with that of the other kinds of cells. Total RNA was obtained from human iPSCs (hiPSCs), human iPSC-derived corneal epithelial cells (hiCECs), human corneal limbal epithelial cells (HCECs), human oral keratinocytes (HOKs), human dermal fibroblasts (HDFs) and six weeks-differentiated hiPSCs (hiPSC-derived ocular surface ectoderm, OSE) using the QIAZol reagent. A microarray analysis using Sure Print G3 human 8x60K slides (Agilent technologies) was performed at Takara Bio (Shiga, Japan).
2016-03-09 | E-GEOD-73971 | biostudies-arrayexpress
Project description:Inflammatory signals must be regulated and kept in check in order to prevent tissue damage. This is especially true in the cornea, where damage can induce loss of transparency, essential for vision. Toll-like receptors (TLRs) are present at the ocular surface and, in addition to being protective against infection, have also been implicated in the pathogenesis of dry eye syndrome, an inflammatory condition that affects millions of individuals in the United States each year. Therefore, an important area of research is the development of new anti-inflammatory therapeutics that limit aberrant ocular surface inflammation. Vitamin D has been studied for its role in suppressing inflammation in other tissues. In previous studies, we have demonstrated that vitamin D is able to decrease proinflammatory mediators induced by TLRs in human corneal epithelial cells (HCEC). Therefore, the goal of the current study was to examine this mechanism further through an evaluation of vitamin Dâs influence on gene expression in two different HCEC cell lines. Microarray comparing hTCEpi, human corneal epithelial cells, treated for 6 hours with Vitamin D (1,25D3) and control (0.1% ethanol) Two-condition arrays: hTCEpi cells were treated with either 100nM 1,25D3 or 0.1% Ethanol for 6h. Two biological replicates, one per array, with a dye swap (technical replicate).
2016-09-01 | E-GEOD-72662 | biostudies-arrayexpress
Project description:Inflammatory signals must be regulated and kept in check in order to prevent tissue damage. This is especially true in the cornea, where damage can induce loss of transparency, essential for vision. Toll-like receptors (TLRs) are present at the ocular surface and, in addition to being protective against infection, have also been implicated in the pathogenesis of dry eye syndrome, an inflammatory condition that affects millions of individuals in the United States each year.  Therefore, an important area of research is the development of new anti-inflammatory therapeutics that limit aberrant ocular surface inflammation. Vitamin D has been studied for its role in suppressing inflammation in other tissues. In previous studies, we have demonstrated that vitamin D is able to decrease proinflammatory mediators induced by TLRs in human corneal epithelial cells (HCEC). Therefore, the goal of the current study was to examine this mechanism further through an evaluation of vitamin Dâ??s influence on gene expression in two different HCEC cell lines. Microarray comparing SV40-HCEC, human corneal epithelial cells, treated for 6 hours with Vitamin D (1,25D3) and control (0.1% ethanol) Two-condition arrays: SV40-HCEC cells were treated with either 100nM 1,25D3 or 0.1% Ethanol for 6h. Two biological replicates, one per array, with a dye swap (technical replicate).
2016-09-01 | E-GEOD-72663 | biostudies-arrayexpress
Project description:Inflammatory signals must be regulated and kept in check in order to prevent tissue damage. This is especially true in the cornea, where damage can induce loss of transparency, essential for vision. Toll-like receptors (TLRs) are present at the ocular surface and, in addition to being protective against infection, have also been implicated in the pathogenesis of dry eye syndrome, an inflammatory condition that affects millions of individuals in the United States each year. Therefore, an important area of research is the development of new anti-inflammatory therapeutics that limit aberrant ocular surface inflammation. Vitamin D has been studied for its role in suppressing inflammation in other tissues. In previous studies, we have demonstrated that vitamin D is able to decrease proinflammatory mediators induced by TLRs in human corneal epithelial cells (HCEC). Therefore, the goal of the current study was to examine this mechanism further through an evaluation of vitamin D’s influence on gene expression in two different HCEC cell lines. Microarray comparing SV40-HCEC, human corneal epithelial cells, treated for 6 hours with Vitamin D (1,25D3) and control (0.1% ethanol)
2016-09-01 | GSE72663 | GEO
Project description:Inflammatory signals must be regulated and kept in check in order to prevent tissue damage. This is especially true in the cornea, where damage can induce loss of transparency, essential for vision. Toll-like receptors (TLRs) are present at the ocular surface and, in addition to being protective against infection, have also been implicated in the pathogenesis of dry eye syndrome, an inflammatory condition that affects millions of individuals in the United States each year. Therefore, an important area of research is the development of new anti-inflammatory therapeutics that limit aberrant ocular surface inflammation. Vitamin D has been studied for its role in suppressing inflammation in other tissues. In previous studies, we have demonstrated that vitamin D is able to decrease proinflammatory mediators induced by TLRs in human corneal epithelial cells (HCEC). Therefore, the goal of the current study was to examine this mechanism further through an evaluation of vitamin D’s influence on gene expression in two different HCEC cell lines. Microarray comparing hTCEpi, human corneal epithelial cells, treated for 6 hours with Vitamin D (1,25D3) and control (0.1% ethanol)
2016-09-01 | GSE72662 | GEO
Project description:To study the development and composition of human ocular surface, we performed single cell (sc) RNA-Seq at key embryonic, fetal and adult stages and generated the first atlas of the corneal and conjunctival cell types from development to adulthood. The conjunctival epithelium is the first to be specified in the epithelial layer , followed by the corneal epithelium and the establishment of proliferative epithelial progenitors, which predate the formation of limbal niche by a few weeks. Bioinformatic comparison of adult cell clusters identified GPHA2,a novel cell-surface marker for quiescent limbal stem cells (qLSCs), whose function is to maintain qLSCs self-renewal. Combining scRNA- and ATAC-Seq analysis, we identified multiple upstream regulators for qLSCs and transit amplifying (TA) cells and demonstrated a close interaction between the immune cells and epithelial stem and progenitor cells in the cornea. Single cell RNA-Seq analysis indicated loss of qLSCs and acquisition of proliferative limbal epithelial progenitor markers during limbal epithelial cell expansion: this phenomenon was independent of culture method used. Extending the single cell analyses to Keratoconus, we were able to reveal activation of collagenase in the corneal stroma and a reduced pool of TA cells in the corneal epithelium as two key mechanistic changes underlying the disease phenotype. Our scRNA-Seq data comparisons of developing and adult cornea and conjunctiva provide a unique resource for defining pathways/genes that could lead to improvement in ex vivo expansion methods for cell based replacement therapies and better understanding and treatment of ocular surface disorders.
2021-04-19 | GSE155683 | GEO
Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in primary and immortalized human corneal epithelial cells. Analysis of regulation of primary and immortalized human corneal epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like corneal cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation and comparitive analysis of numerous genes in response to dihydrotestosterone incubation in primary and immortalized human corneal epithelial cells.
2011-03-31 | GSE18093 | GEO
Project description:The rapid and effective regeneration of corneal epithelial cells depends on limbal stem cells (LSCs). The LSCs of mouse can be subdivided into quiescent LSCs (located on the outer limbus, qLSCs) and active LSCs (located on the inner limbus, aLSCs). Here, we used single-cell RNA sequencing to decipher the transcriptional changes in qLSCs and aLSCs and their niche regulations during the corneal wound healing, and reconstructed the pseudotime trajectory and differentiation of LSCs. Our comparative study identified a transcription factor Creb5, expressed in LSCs, that was significantly upregulated after corneal epithelial injury, and the loss-of-function experiments revealed that silencing Creb5 delayed the corneal epithelial healing. Besides, we predicted a significant increase in the number of ligand-receptor pairs for intercellular communications during corneal epithelial wound healing, especially between immune cells and LSCs, implying the participation of various niche cells in limbal stem cell kinetics during corneal epithelial regeneration. Overall, our research reveals numerous findings on the behavior and functionality of LSCs during corneal wound healing, providing reference for the discovery of mechanisms and potential clinical interventions of ocular surface reconstruction.
2024-07-10 | GSE247392 | GEO
Project description:Diabetic keratopathy(DK) is a common ocular complication of diabetes that seriously threatens diabetic patients' vision. Here, by sequencing of microRNAs (miRNAs) from diabetic and normal TG tissues, we aimed to uncover potential miRNAs involved in the pathogenesis of diabetic corneal neuropathy.
2023-10-18 | GSE245193 | GEO