Molecular signatures and biological pathway profiles of human corneal epithelial progenitor cells

Identification and isolation of adult stem cells are still challenging for stem cell biologists. For example, no consensus exists yet regarding definitive markers for corneal epithelial stem cells, which have been identified to reside in the limbus for two decades. This study characterized the molecular signatures and biological pathways of limbal epithelial progenitors, the rapid adherent cells (RAC) isolated by adhesion on collagen IV, using human genome microarrays, real-time PCR and immunofluorescent staining. The microarrays produced highly reproducible data not only for all gene transcripts, but also for significantly changed genes, although the total 12 samples of 3 cell populations in 2 arrays were isolated from 4 separate experiments at different time period. The hierarchical clustering heatmap visually revealed that RAC progenitor population displayed distinguishably characteristic gene expression profile. With verification of 27 important genes by quantitative real-time PCR, the microarray data not only confirm the expression patterns of 15 known genes as stem cell associated markers representing limbal stem cell phenotype, but also identified many significantly regulated genes expressed by limbal progenitor cells. Transcription factor TCF4 and cell surface protein SPRRs were identified as potentially positive or negative markers, respectively, for corneal epithelial progenitor cells. Using GenMAPP and MAPPFinder, we have identified three patterns of biological pathway profiles, overexpressed, underexpressed and balanced, by RAC progenitors based on gene ontology categories. These genes and related pathways are interesting targets for further identification and isolation of limbal stem cells as well as other tissue-specific adult stem cells.