Similarity of mRNA phenotypes of morphologically normal macular and peripheral retinal pigment epithelial cells in older human eyes

Kazuki Ishibashi, Jane Tian, James Handa

Research output: Contribution to journalArticle

Abstract

PURPOSE. To determine the expression profiles of morphologically normal human retinal pigment epithelial (RPE) cells that originate from the macula and periphery. METHODS. Morphologically normal RPE cells from 15 human globes from donors aged 52 to 82 years old were laser capture microdissected. Total RNA from 5000 cells was SMART amplified, [33]P-labeled, and hybridized to a cDNA array containing 4325 known genes. Expression profiles were analyzed by hierarchical cluster analysis, Prediction Analysis of Microarrays (PAM), and Significance Analysis for Microarrays (SAM). Differentially expressed genes were evaluated further by real time RT-PCR. RESULTS. The overall expression profiles of RPE cells from the macula and periphery were similar. Unsupervised and supervised hierarchical cluster analysis showed that patient genotype was a stronger separating factor than topographical location. SAM analysis identified 11 genes that were underexpressed by macular RPE cells. The expression patterns of these 11 genes were confirmed by real time RT-PCR, with 5 genes reaching statistical significance. CONCLUSIONS. Whereas the overall expression profiles were similar between cells from the macula and periphery, subtle differential expression of five genes could contribute to RPE phenotypic differences based on topographic location.

Original languageEnglish (US)
Pages (from-to)3291-3301
Number of pages11
JournalInvestigative Ophthalmology and Visual Science
Volume45
Issue number9
DOIs
StatePublished - Sep 2004

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Retinal Pigments
Epithelial Cells
Phenotype
Microarray Analysis
Messenger RNA
Genes
Cluster Analysis
Real-Time Polymerase Chain Reaction
Oligonucleotide Array Sequence Analysis
Lasers
Genotype
Tissue Donors
RNA
Gene Expression

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Similarity of mRNA phenotypes of morphologically normal macular and peripheral retinal pigment epithelial cells in older human eyes. / Ishibashi, Kazuki; Tian, Jane; Handa, James.

In: Investigative Ophthalmology and Visual Science, Vol. 45, No. 9, 09.2004, p. 3291-3301.

Research output: Contribution to journalArticle

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abstract = "PURPOSE. To determine the expression profiles of morphologically normal human retinal pigment epithelial (RPE) cells that originate from the macula and periphery. METHODS. Morphologically normal RPE cells from 15 human globes from donors aged 52 to 82 years old were laser capture microdissected. Total RNA from 5000 cells was SMART amplified, [33]P-labeled, and hybridized to a cDNA array containing 4325 known genes. Expression profiles were analyzed by hierarchical cluster analysis, Prediction Analysis of Microarrays (PAM), and Significance Analysis for Microarrays (SAM). Differentially expressed genes were evaluated further by real time RT-PCR. RESULTS. The overall expression profiles of RPE cells from the macula and periphery were similar. Unsupervised and supervised hierarchical cluster analysis showed that patient genotype was a stronger separating factor than topographical location. SAM analysis identified 11 genes that were underexpressed by macular RPE cells. The expression patterns of these 11 genes were confirmed by real time RT-PCR, with 5 genes reaching statistical significance. CONCLUSIONS. Whereas the overall expression profiles were similar between cells from the macula and periphery, subtle differential expression of five genes could contribute to RPE phenotypic differences based on topographic location.",
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N2 - PURPOSE. To determine the expression profiles of morphologically normal human retinal pigment epithelial (RPE) cells that originate from the macula and periphery. METHODS. Morphologically normal RPE cells from 15 human globes from donors aged 52 to 82 years old were laser capture microdissected. Total RNA from 5000 cells was SMART amplified, [33]P-labeled, and hybridized to a cDNA array containing 4325 known genes. Expression profiles were analyzed by hierarchical cluster analysis, Prediction Analysis of Microarrays (PAM), and Significance Analysis for Microarrays (SAM). Differentially expressed genes were evaluated further by real time RT-PCR. RESULTS. The overall expression profiles of RPE cells from the macula and periphery were similar. Unsupervised and supervised hierarchical cluster analysis showed that patient genotype was a stronger separating factor than topographical location. SAM analysis identified 11 genes that were underexpressed by macular RPE cells. The expression patterns of these 11 genes were confirmed by real time RT-PCR, with 5 genes reaching statistical significance. CONCLUSIONS. Whereas the overall expression profiles were similar between cells from the macula and periphery, subtle differential expression of five genes could contribute to RPE phenotypic differences based on topographic location.

AB - PURPOSE. To determine the expression profiles of morphologically normal human retinal pigment epithelial (RPE) cells that originate from the macula and periphery. METHODS. Morphologically normal RPE cells from 15 human globes from donors aged 52 to 82 years old were laser capture microdissected. Total RNA from 5000 cells was SMART amplified, [33]P-labeled, and hybridized to a cDNA array containing 4325 known genes. Expression profiles were analyzed by hierarchical cluster analysis, Prediction Analysis of Microarrays (PAM), and Significance Analysis for Microarrays (SAM). Differentially expressed genes were evaluated further by real time RT-PCR. RESULTS. The overall expression profiles of RPE cells from the macula and periphery were similar. Unsupervised and supervised hierarchical cluster analysis showed that patient genotype was a stronger separating factor than topographical location. SAM analysis identified 11 genes that were underexpressed by macular RPE cells. The expression patterns of these 11 genes were confirmed by real time RT-PCR, with 5 genes reaching statistical significance. CONCLUSIONS. Whereas the overall expression profiles were similar between cells from the macula and periphery, subtle differential expression of five genes could contribute to RPE phenotypic differences based on topographic location.

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