Serial microanalysis of renal transcriptomes

Bérangère Virlon*,, Lydie Cheval*,, Jean-Marie Buhler, Emmanuelle Billon*, Alain Doucet*, and Jean-Marc Elalouf*,§

* Département de Biologie Cellulaire et Moléculaire, Service de Biologie Cellulaire, Centre National de la Recherche Scientifique Unité de Recherche Associée 1859; and Service de Biochimie et de Génétique Moléculaire, Commissariat à l'Energie Atomique Saclay, 91191 Gif-sur-Yvette Cedex, France

PNAS Vol. 96, Issue 26, 15286-15291, December 21, 1999

Edited by Bert Vogelstein, Johns Hopkins Oncology Center, Baltimore, MD, and approved October 19, 1999 (received for review August 3, 1999)

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Large-scale gene expression studies can now be routinely performed on macroamounts of cells, but it is unclear to which extentcurrent methods are valuable for analyzing complex tissues. Inthe present study, we used the method of serial analysis of geneexpression (SAGE) for quantitative mRNA profiling in the mousekidney. We first performed SAGE at the whole-kidney level by sequencing12,000 mRNA tags. Most abundant tags corresponded to transcriptswidely distributed or enriched in the predominant kidney epithelialcells (proximal tubular cells), whereas transcripts specific forminor cell types were barely evidenced. To better explore suchcells, we set up a SAGE adaptation for downsized extracts, enablinga 1,000-fold reduction of the amount of starting material. Thepotential of this approach was evaluated by studying gene expressionin microdissected kidney tubules (50,000 cells). Specific geneexpression profiles were obtained, and known markers (e.g., uromodulinin the thick ascending limb of Henle's loop and aquaporin-2 inthe collecting duct) were found appropriately enriched. In addition,several enriched tags had no databank match, suggesting that theycorrespond to unknown or poorly characterized transcripts withspecific tissue distribution. It is concluded that SAGE adaptationfor downsized extracts makes possible large-scale quantitativegene expression measurements in small biological samples and willhelp to study the tissue expression and function of genes notevidenced with other high-throughputmethods.

B.V. and L.C. contributed equally to thiswork.

To whom reprint requests should be addressed. E-mail: elalouf@dsvidf.cea.fr.

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