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Jorge E. Valdez, Judith Zavala, Victor Treviño, Emmanuel Martínez; Over-representation Preliminary Analysis Between Expressed Genes In Corneal Endothelium And Mesenchymal Stem Cells. Invest. Ophthalmol. Vis. Sci. 2012;53(14):6008.
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To determine with a preliminary analysis the main gene expression pattern difference between corneal endothelial cells and adipose mesenchymal stem cells (MSC) in order to set a baseline for in vitro differentiation assays.
One sample of healthy human corneal endothelium and four of human adipose mesenchymal stem cells run with the same platform were obtained from GEO database. The average of difference expression between samples was calculated and a list of 195 of genes with an absolute difference above 0.4 was obtained. An over-representation analysis was made in order to know related pathways, gene ontology and transcription factors.
Among the 195 significant different genes, 98 were related to CHX10 gene (P value = 1.8x10-4), associated to visual perception, camera-type eye development and retinal bipolar neuron differentiation. 107 genes, including BDNF, were related to CART1 (P value = 1.3x10-4), a gene involved in the brain development. 125 genes, like TGFβ2, were related to POU3F2 gene (P value = 4.7x10-4), a CNS-specific transcription factor involved in neurogenesis. TGFβ2 along with BDNF was found with higher expression in corneal endothelium between the genes related with the regulation of cell proliferation. 114 genes were associated to Pax6 gene (P value = 4.8x10-3), implicated in corneal development during embryogenesis. Pax6 was slightly over-expressed in corneal endothelium. 9 genes were found to be related with positive regulation of cell migration (P value = 4.1x10-4) with higher expression in corneal endothelium, like endothelin1 and heparin-binding EGF-like growth factor. 15 genes were found to be associated with positive regulation of developmental process (P value = 9x10-4), like the fibroblast growth factor 9 (FGF9) and histone deacetylase 9, with higher expression in MSC.
This preliminary analysis provides a general idea of the difference in the pattern gene expression between corneal endothelium and mesenchymal stem cells in and set the guideline to do an extensive study with a larger number of samples, as very little information is available in this field.
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