Expression profiling of human Schlemm’s canal endothelial cells from eyes with and without glaucoma

Jingwen Cai, Kristin M. Perkumas, Xuejun Qin, Michael A. Hauser, W. Daniel Stamer, Yutao Liu

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

PURPOSE. Ocular hypertension is a major risk factor for glaucoma and the inner wall of Schlemm’s canal (SC) endothelia participates in the regulation of aqueous humor outflow resistance. This study aimed to identify differentially expressed genes in primary cultures of SC cells from glaucoma patients. METHODS. This study examined SC samples from three glaucoma cases and four controls. Schlemm’s canal cells were isolated from eight different postmortem human eyes. Total RNA was extracted, labeled, and hybridized to Illumina HumanWG-6 BeadChips containing probes for approximately 47,000 human transcripts. After extracting the data using Illumina GenomeStudio software, the data were normalized and analyzed using the R package limma in Bioconductor. Using Protein ANalysis THrough Evolutionary Relationships (PANTHER) software, gene ontology analysis of highly expressed genes was executed in controls and glaucoma groups separately. Pathway analysis was performed with differentially expressed genes using WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). Selected genes were validated using droplet digital PCR (ddPCR). RESULTS. Gene ontology analysis indicated similar functional categories in cases and controls. Differential analysis identified a total of 113 genes with at least 2-fold expression changes in cases. Pathway analysis indicated significant enrichment of genes in cell adhesion, heparin binding, glycosaminoglycan binding, filopodium, and extracellular matrix remodeling. Eighteen selected genes with differential expression were successfully validated using ddPCR. CONCLUSIONS. This study represents the first genome-wide expression study of human primary SC cells from glaucoma patients and provides a potential list of targets regulating SC cell stiffness and pore formation, eventually the outflow resistance in glaucoma individuals.

Original languageEnglish (US)
Pages (from-to)6747-6753
Number of pages7
JournalInvestigative Ophthalmology and Visual Science
Volume56
Issue number11
DOIs
StatePublished - Oct 1 2015

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Glaucoma
Endothelial Cells
Genes
Gene Ontology
Software
Polymerase Chain Reaction
Ocular Hypertension
Pseudopodia
Aqueous Humor
Glycosaminoglycans
Cell Adhesion
Endothelium
Extracellular Matrix
Heparin
Genome
RNA
Control Groups
Proteins

Keywords

  • Aqueous flow
  • Gene expression
  • Glaucoma
  • Schlemm’s canal

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

Expression profiling of human Schlemm’s canal endothelial cells from eyes with and without glaucoma. / Cai, Jingwen; Perkumas, Kristin M.; Qin, Xuejun; Hauser, Michael A.; Daniel Stamer, W.; Liu, Yutao.

In: Investigative Ophthalmology and Visual Science, Vol. 56, No. 11, 01.10.2015, p. 6747-6753.

Research output: Contribution to journalArticle

Cai, Jingwen ; Perkumas, Kristin M. ; Qin, Xuejun ; Hauser, Michael A. ; Daniel Stamer, W. ; Liu, Yutao. / Expression profiling of human Schlemm’s canal endothelial cells from eyes with and without glaucoma. In: Investigative Ophthalmology and Visual Science. 2015 ; Vol. 56, No. 11. pp. 6747-6753.
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abstract = "PURPOSE. Ocular hypertension is a major risk factor for glaucoma and the inner wall of Schlemm’s canal (SC) endothelia participates in the regulation of aqueous humor outflow resistance. This study aimed to identify differentially expressed genes in primary cultures of SC cells from glaucoma patients. METHODS. This study examined SC samples from three glaucoma cases and four controls. Schlemm’s canal cells were isolated from eight different postmortem human eyes. Total RNA was extracted, labeled, and hybridized to Illumina HumanWG-6 BeadChips containing probes for approximately 47,000 human transcripts. After extracting the data using Illumina GenomeStudio software, the data were normalized and analyzed using the R package limma in Bioconductor. Using Protein ANalysis THrough Evolutionary Relationships (PANTHER) software, gene ontology analysis of highly expressed genes was executed in controls and glaucoma groups separately. Pathway analysis was performed with differentially expressed genes using WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). Selected genes were validated using droplet digital PCR (ddPCR). RESULTS. Gene ontology analysis indicated similar functional categories in cases and controls. Differential analysis identified a total of 113 genes with at least 2-fold expression changes in cases. Pathway analysis indicated significant enrichment of genes in cell adhesion, heparin binding, glycosaminoglycan binding, filopodium, and extracellular matrix remodeling. Eighteen selected genes with differential expression were successfully validated using ddPCR. CONCLUSIONS. This study represents the first genome-wide expression study of human primary SC cells from glaucoma patients and provides a potential list of targets regulating SC cell stiffness and pore formation, eventually the outflow resistance in glaucoma individuals.",
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N2 - PURPOSE. Ocular hypertension is a major risk factor for glaucoma and the inner wall of Schlemm’s canal (SC) endothelia participates in the regulation of aqueous humor outflow resistance. This study aimed to identify differentially expressed genes in primary cultures of SC cells from glaucoma patients. METHODS. This study examined SC samples from three glaucoma cases and four controls. Schlemm’s canal cells were isolated from eight different postmortem human eyes. Total RNA was extracted, labeled, and hybridized to Illumina HumanWG-6 BeadChips containing probes for approximately 47,000 human transcripts. After extracting the data using Illumina GenomeStudio software, the data were normalized and analyzed using the R package limma in Bioconductor. Using Protein ANalysis THrough Evolutionary Relationships (PANTHER) software, gene ontology analysis of highly expressed genes was executed in controls and glaucoma groups separately. Pathway analysis was performed with differentially expressed genes using WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). Selected genes were validated using droplet digital PCR (ddPCR). RESULTS. Gene ontology analysis indicated similar functional categories in cases and controls. Differential analysis identified a total of 113 genes with at least 2-fold expression changes in cases. Pathway analysis indicated significant enrichment of genes in cell adhesion, heparin binding, glycosaminoglycan binding, filopodium, and extracellular matrix remodeling. Eighteen selected genes with differential expression were successfully validated using ddPCR. CONCLUSIONS. This study represents the first genome-wide expression study of human primary SC cells from glaucoma patients and provides a potential list of targets regulating SC cell stiffness and pore formation, eventually the outflow resistance in glaucoma individuals.

AB - PURPOSE. Ocular hypertension is a major risk factor for glaucoma and the inner wall of Schlemm’s canal (SC) endothelia participates in the regulation of aqueous humor outflow resistance. This study aimed to identify differentially expressed genes in primary cultures of SC cells from glaucoma patients. METHODS. This study examined SC samples from three glaucoma cases and four controls. Schlemm’s canal cells were isolated from eight different postmortem human eyes. Total RNA was extracted, labeled, and hybridized to Illumina HumanWG-6 BeadChips containing probes for approximately 47,000 human transcripts. After extracting the data using Illumina GenomeStudio software, the data were normalized and analyzed using the R package limma in Bioconductor. Using Protein ANalysis THrough Evolutionary Relationships (PANTHER) software, gene ontology analysis of highly expressed genes was executed in controls and glaucoma groups separately. Pathway analysis was performed with differentially expressed genes using WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). Selected genes were validated using droplet digital PCR (ddPCR). RESULTS. Gene ontology analysis indicated similar functional categories in cases and controls. Differential analysis identified a total of 113 genes with at least 2-fold expression changes in cases. Pathway analysis indicated significant enrichment of genes in cell adhesion, heparin binding, glycosaminoglycan binding, filopodium, and extracellular matrix remodeling. Eighteen selected genes with differential expression were successfully validated using ddPCR. CONCLUSIONS. This study represents the first genome-wide expression study of human primary SC cells from glaucoma patients and provides a potential list of targets regulating SC cell stiffness and pore formation, eventually the outflow resistance in glaucoma individuals.

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