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J. Biol. Chem., Vol. 281, Issue 28, 19600-19609, July 14, 2006

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Transcriptional Profiling of Enriched Populations of Stem Cells Versus Transient Amplifying Cells

A COMPARISON OF LIMBAL AND CORNEAL EPITHELIAL BASAL CELLS^*

Mingyuan Zhou, Xin-min Li, and Robert M. Lavker¹

From the Department of Dermatology, Feinberg School of Medicine, Chicago, Illinois 60611 and the Department of Genetic Analysis, University of Chicago, Chicago, Illinois 60637

The basal layer of limbal and central corneal epithelium is enriched in stem cells and transient amplifying cells, respectively. This physical separation of stem and transient amplifying cells makes the limbal/corneal epithelium an exceptionally suitable system for isolating basal cells enriched in these two proliferative populations. Prior attempts to isolate epithelial stem cells used methods such as proteolytic tissue dissociation and cell sorting that could potentially alter their gene expression profile. Using laser capture microdissection, we were able to isolate resting limbal and corneal basal cells from frozen sections with minimal tissue processing, thereby improving the yield and quality of RNA. Analyses of RNA isolated from 300 limbal and corneal basal cells from eight mice revealed a set of 100 genes that are differentially expressed in limbal cells versus corneal epithelial basal cells. Semiquantitative reverse transcription-PCR confirmed the up-regulation of three limbal and three corneal genes. LacZ identification of epiregulin from epiregulin-null mice and immunohistochemical staining of wild type mice confirmed that epiregulin, one of the limbal epithelium-enriched genes, was associated with the limbal epithelial basal cells. Within the limbal and corneal basal cells, we detected previously unknown genes that were differentially expressed in these two regions that contribute further to our understanding of the unique heterogeneity of these two closely related basal cell populations. Our findings indicate that we can obtain accurate gene expression profiles of the stem cell-enriched limbal basal cell population in their "natural" quiescent state.

Received for publication, January 25, 2006 , and in revised form, April 5, 2006.

^* This work was supported by National Institutes of Health Grants EY06769 and EY13711 (to R. M. L.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence should be addressed: Dept. of Dermatology, Northwestern University School of Medicine, 303 E. Chicago Ave., Ward-9-125, Chicago, IL 60611. Tel.: 312-503-4315; Fax: 312-503-4325; E-mail: r-lavker{at}northwestern.edu.

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