Comparative global gene expression profile of human limbal stromal cells, bone marrow mesenchymal stromal cells, adipose-derived mesenchymal stromal cells and foreskin fibroblasts

Abstract

Background : Limbal epithelial stem cells (LESC) have great potential in treating the blindness caused by corneal damage. LESC are maintained in stem cell niche called Palisade of Vogt. Limbal stromal (LS) cells are critical component of LESC niche and help in their self renewal. These cells resemble mesenchymal stromal/stem cells with multilineage differentiation potential. However little is known about their gene expression profile compared to MSC derived from various sources. Methods : In this study, we compared the gene expression profile of LS cells expanded in two different culture conditions: basal media with bFGF, LIF and matrigel (LS-matrigel), as well as basal media with 10% FBS (LS-FBS). In addition, gene expression profile of LS-FBS cells were compared to bone marrow, adipose-derived MSC and foreskin fibroblasts. Total RNA was extracted from various cell types upon achieving confluency and subjected to microarray experiments (Agilent platform) using Human GE 8x60k gene chips. Data analysis was done with GeneSpring software. Results : LS cells cultured in matrigel system showed upregulation of 871 genes as compared to LS-FBS and 58 genes were consistently differentially expressed in LS-FBS as compared to other cell types. Despite many long intergenic non-coding RNA and function unknown genes, differentially expressed genes represent gene ontology for cell signaling molecules including various growth factors, cell metabolism and extracellular matrix components for various biological processes. Samples from the same source were closely clustered by hierachical clustering analysis. Conclusions : The two culture conditions used in the study affected the gene expression profile of LS cells significantly. The LS cells showed distinct molecular signature as compared to MSC from various other sources. This comparative study will help in understanding the limbal stem cell niche biology and the novel set of genes could be used as biomarkers for LS cells.